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Majethia P, Kaur N, Mascarenhas S, Rao LP, Pande S, Narayanan DL, Bhat V, Nayak SS, Nair KV, Prasannakumar AP, Chaurasia A, Hunakunti B, Jadhav N, Farooqui S, Yeole M, Kothiwale V, Naik R, Bhat V, Aroor S, Lewis L, Purkayastha J, Bhat YR, Praveen BK, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Siddiqui S, Bielas S, Girisha KM, Sharma S, Shukla A. Genetic and phenotypic landscape of pediatric-onset epilepsy in 142 Indian families: Counseling and therapeutic implications. Clin Genet 2024; 105:639-654. [PMID: 38374498 PMCID: PMC7615923 DOI: 10.1111/cge.14495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024]
Abstract
The application of genomic technologies has led to unraveling of the complex genetic landscape of disorders of epilepsy, gaining insights into their underlying disease mechanisms, aiding precision medicine, and providing informed genetic counseling. We herein present the phenotypic and genotypic insights from 142 Indian families with epilepsy with or without comorbidities. Based on the electroclinical findings, epilepsy syndrome diagnosis could be made in 44% (63/142) of the families adopting the latest proposal for the classification by the ILAE task force (2022). Of these, 95% (60/63) of the families exhibited syndromes with developmental epileptic encephalopathy or progressive neurological deterioration. A definitive molecular diagnosis was achieved in 74 of 142 (52%) families. Infantile-onset epilepsy was noted in 81% of these families (61/74). Fifty-five monogenic, four chromosomal, and one imprinting disorder were identified in 74 families. The genetic variants included 65 (96%) single-nucleotide variants/small insertion-deletions, 1 (2%) copy-number variant, and 1 (2%) triplet-repeat expansion in 53 epilepsy-associated genes causing monogenic disorders. Of these, 35 (52%) variants were novel. Therapeutic implications were noted in 51% of families (38/74) with definitive diagnosis. Forty-one out of 66 families with monogenic disorders exhibited autosomal recessive and inherited autosomal dominant disorders with high risk of recurrence.
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Affiliation(s)
- Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shalini S. Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Vijay Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Adarsh Pooradan Prasannakumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheeba Farooqui
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Mayuri Yeole
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vishaka Kothiwale
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rohit Naik
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Veena Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jayashree Purkayastha
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Y. Ramesh Bhat
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B. K. Praveen
- Department of Pediatrics, Father Muller Medical College Hospital, Mangalore, India
| | - B. L. Yatheesha
- Paediatric neurology, Dheemahi Child Neurology and Development Center, Shimoga, India
| | - Siddaramappa J. Patil
- Division of Medical Genetics, Narayana Hrudayalaya Hospitals/Mazumdar-Shaw Medical Center, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Hyderabad, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children’s Hospital, New Delhi, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Kakar N, Rehman FU, Kaur R, Bhavani GS, Goyal M, Shah H, Kaur K, Sodhi KS, Kubisch C, Borck G, Panigrahi I, Girisha KM, Kornak U, Spielmann M. Multi-gene panel sequencing in highly consanguineous families and patients with congenital forms of skeletal dysplasias. Clin Genet 2024. [PMID: 38378010 DOI: 10.1111/cge.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Skeletal dysplasias (SKDs) are a heterogeneous group of more than 750 genetic disorders characterized by abnormal development, growth, and maintenance of bones or cartilage in the human skeleton. SKDs are often caused by variants in early patterning genes and in many cases part of multiple malformation syndromes and occur in combination with non-skeletal phenotypes. The aim of this study was to investigate the underlying genetic cause of congenital SKDs in highly consanguineous Pakistani families, as well as in sporadic and familial SKD cases from India using multigene panel sequencing analysis. Therefore, we performed panel sequencing of 386 bone-related genes in 7 highly consanguineous families from Pakistan and 27 cases from India affected with SKDs. In the highly consanguineous families, we were able to identify the underlying genetic cause in five out of seven families, resulting in a diagnostic yield of 71%. Whereas, in the sporadic and familial SKD cases, we identified 12 causative variants, corresponding to a diagnostic yield of 44%. The genetic heterogeneity in our cohorts was very high and we were able to detect various types of variants, including missense, nonsense, and frameshift variants, across multiple genes known to cause different types of SKDs. In conclusion, panel sequencing proved to be a highly effective way to decipher the genetic basis of SKDs in highly consanguineous families as well as sporadic and or familial cases from South Asia. Furthermore, our findings expand the allelic spectrum of skeletal dysplasias.
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Affiliation(s)
- Naseebullah Kakar
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Fazal Ur Rehman
- Department of Pathology, Bolan Medical College, Quetta, Pakistan
| | - Ramandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Manisha Goyal
- Pediatrics Genetic & Research Laboratory, Department of Pediatrics, Lok Nayak Hospital, New Delhi, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
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Sithambaram S, Jacob P, Neethukrishna K, Bhavani GS, Dalal A, Shah H, Girisha KM. PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome in an Indian patient. Am J Med Genet A 2024:e63566. [PMID: 38357848 DOI: 10.1002/ajmg.a.63566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/16/2024]
Abstract
PRKACA-related, atrial defects-polydactyly-multiple congenital malformation syndrome is a recently described skeletal ciliopathy, which is caused by disease-causing variants in PRKACA. The primary phenotypic description includes atrial septal defects, and limb anomalies including polydactyly and short limbs. To date, only four molecularly proven patients have been reported in the literature with a recurrent variant, c.409G>A p.Gly137Arg in PRKACA. In this study, we report the fifth affected individual with the same variant and review the clinical features and radiographic findings of this rare syndrome.
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Affiliation(s)
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Hitesh Shah
- Department of Pediatric Orthopaedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
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Purushothama G, Bhavani GSL, Shah H, Girisha KM, Handattu K. Expansion of Phenotypic Spectrum in Hyperphosphatemic Familial Tumoral Calcinosis. Indian Pediatr 2024; 61:186-188. [PMID: 38217273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Affiliation(s)
- Greeshma Purushothama
- Department of Medical Genetics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, Karnataka
| | - Gandham Sri Lakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, Karnataka
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, Karnataka
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, Karnataka
| | - Koushik Handattu
- Department of Pediatrics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, Karnataka.
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Pande S, Majethia P, Nair K, Rao LP, Mascarenhas S, Kaur N, do Rosario MC, Neethukrishna K, Chaurasia A, Hunakunti B, Jadhav N, Xavier S, Kumar J, Bhat V, Bhavani GS, Narayanan DL, Yatheesha BL, Patil SJ, Nampoothiri S, Kamath N, Aroor S, Bhat Y R, Lewis LE, Sharma S, Bajaj S, Sankhyan N, Siddiqui S, Nayak SS, Bielas S, Girisha KM, Shukla A. De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India. Eur J Hum Genet 2023:10.1038/s41431-023-01513-7. [PMID: 38114583 DOI: 10.1038/s41431-023-01513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/21/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
The contribution of de novo variants as a cause of intellectual disability (ID) is well established in several cohorts reported from the developed world. However, the genetic landscape as well as the appropriate testing strategies for identification of de novo variants of these disorders remain largely unknown in low-and middle-income countries like India. In this study, we delineate the clinical and genotypic spectrum of 54 families (55 individuals) with syndromic ID harboring rare de novo variants. We also emphasize on the effectiveness of singleton exome sequencing as a valuable tool for diagnosing these disorders in resource limited settings. Overall, 46 distinct disorders were identified encompassing 46 genes with 51 single-nucleotide variants and/or indels and two copy-number variants. Pathogenic variants were identified in CREBBP, TSC2, KMT2D, MECP2, IDS, NIPBL, NSD1, RIT1, SOX10, BRWD3, FOXG1, BCL11A, KDM6B, KDM5C, SETD5, QRICH1, DCX, SMARCD1, ASXL1, ASXL3, AKT3, FBN2, TCF12, WASF1, BRAF, SMARCA4, SMARCA2, TUBG1, KMT2A, CTNNB1, DLG4, MEIS2, GATAD2B, FBXW7, ANKRD11, ARID1B, DYNC1H1, HIVEP2, NEXMIF, ZBTB18, SETD1B, DYRK1A, SRCAP, CASK, L1CAM, and KRAS. Twenty-four of these monogenic disorders have not been previously reported in the Indian population. Notably, 39 out of 53 (74%) disease-causing variants are novel. These variants were identified in the genes mainly encoding transcriptional and chromatin regulators, serine threonine kinases, lysosomal enzymes, molecular motors, synaptic proteins, neuronal migration machinery, adhesion molecules, structural proteins and signaling molecules.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Namanpreet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Kausthubham Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ankur Chaurasia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Bhagesh Hunakunti
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nalesh Jadhav
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sruthy Xavier
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jeevan Kumar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - B L Yatheesha
- Dheemahi Child Neurology and Development Center, Shivamogga, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran Aroor
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie E Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Neurology Division, Department of Pediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | | | - Naveen Sankhyan
- Pediatric Neurology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Shahyan Siddiqui
- Department of Neuro and Vascular Interventional Radiology, Yashoda Hospitals, Secunderabad, Hyderabad, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- Suma Genomics Private Limited, Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
- Department of Genetics, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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Pande S, Mascarenhas S, Venkatraman A, Bhat V, Narayanan DL, Siddiqui S, Bielas S, Girisha KM, Shukla A. Further validation of craniosynostosis as a part of phenotypic spectrum of BCL11B-related BAFopathy. Am J Med Genet A 2023; 191:2175-2180. [PMID: 37337996 PMCID: PMC10448182 DOI: 10.1002/ajmg.a.63330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/25/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Heterozygous disease-causing variants in BCL11B are the basis of a rare neurodevelopmental syndrome with craniofacial and immunological involvement. Isolated craniosynostosis, without systemic or immunological findings, has been reported in one of the 17 individuals reported with this disorder till date. We report three additional individuals harboring de novo heterozygous frameshift variants, all lying in the exon 4 of BCL11B. All three individuals presented with the common findings of this disorder i.e. developmental delay, recurrent infections with immunologic abnormalities and facial dysmorphism. Notably, craniosynostosis of variable degree was seen in all three individuals. We, thus add to the evolving genotypes and phenotypes of BCL11B-related BAFopathy and also review the clinical, genomic spectrum along with the underlying disease mechanisms of this disorder.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Selinda Mascarenhas
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Aishwarya Venkatraman
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Vivekananda Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Shahyan Siddiqui
- Department of Neuroimaging and Interventional Radiology, STAR Institute of Neurosciences, STAR hospitals, Hyderabad, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal
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do Rosario MC, Purushothama G, Narayanan DL, Siddiqui S, Girisha KM, Shukla A. Extended analysis of exome sequencing data reveals a novel homozygous deletion of exons 3 and 4 in FUCA1 gene causing fucosidosis in an Indian family. Clin Dysmorphol 2023; 32:112-115. [PMID: 36876340 PMCID: PMC10238607 DOI: 10.1097/mcd.0000000000000452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Michelle C. do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Greeshma Purushothama
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
- DBT Wellcome Trust India Alliance Early Career Clinical and Public Health Research Fellow
| | - Shahyan Siddiqui
- Department of Neuroimaging and Interventional Radiology, STAR Institute of Neurosciences, STAR Hospitals, Hyderabad, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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do Rosario MC, Bey GR, Nmezi B, Liu F, Oranburg T, Cohen ASA, Coffman KA, Brown MR, Kiselyov K, Waisfisz Q, Flohil MT, Siddiqui S, Rosenfeld JA, Iglesias A, Girisha KM, Wolf NI, Padiath QS, Shukla A. Variants in the zinc transporter TMEM163 cause a hypomyelinating leukodystrophy. Brain 2022; 145:4202-4209. [PMID: 35953447 PMCID: PMC10200305 DOI: 10.1093/brain/awac295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/12/2022] [Accepted: 07/31/2022] [Indexed: 11/12/2022] Open
Abstract
Hypomyelinating leukodystrophies comprise a subclass of genetic disorders with deficient myelination of the CNS white matter. Here we report four unrelated families with a hypomyelinating leukodystrophy phenotype harbouring variants in TMEM163 (NM_030923.5). The initial clinical presentation resembled Pelizaeus-Merzbacher disease with congenital nystagmus, hypotonia, delayed global development and neuroimaging findings suggestive of significant and diffuse hypomyelination. Genomic testing identified three distinct heterozygous missense variants in TMEM163 with two unrelated individuals sharing the same de novo variant. TMEM163 is highly expressed in the CNS particularly in newly myelinating oligodendrocytes and was recently revealed to function as a zinc efflux transporter. All the variants identified lie in highly conserved residues in the cytoplasmic domain of the protein, and functional in vitro analysis of the mutant protein demonstrated significant impairment in the ability to efflux zinc out of the cell. Expression of the mutant proteins in an oligodendroglial cell line resulted in substantially reduced mRNA expression of key myelin genes, reduced branching and increased cell death. Our findings indicate that variants in TMEM163 cause a hypomyelinating leukodystrophy and uncover a novel role for zinc homeostasis in oligodendrocyte development and myelin formation.
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Affiliation(s)
- Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Guillermo Rodriguez Bey
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Bruce Nmezi
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Fang Liu
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Talia Oranburg
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ana S A Cohen
- Genomic Medicine Center, Children’s Mercy, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy, Kansas City, MO 64108, USA
- School of Medicine Serves, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Keith A Coffman
- Division of Neurology, Movement Disorders Clinic, Tourette Syndrome Center of Excellence, Children’s Mercy Hospital, Kansas City, Missouri, USA
| | - Maya R Brown
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kirill Kiselyov
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam University Medical Centers, VU University Amsterdam, and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Myrthe T Flohil
- Department of Neurology, Noordwest ziekenhuisgroep, Wilhelminalaan Alkmaar, The Netherlands
| | - Shahyan Siddiqui
- Department of Neuroimaging and Interventional Radiology, STAR Institute of Neurosciences, STAR Hospitals, Hyderabad, India
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Nicole I Wolf
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma’s Children’s Hospital, and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Amsterdam, The Netherlands
| | - Quasar Saleem Padiath
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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9
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do Rosario MC, Kaur P, Girisha KM, Bielas S, Shukla A. Homozygous variant p.(Arg163Trp) in PIGH causes glycosylphosphatidylinositol biosynthesis defect with epileptic encephalopathy and delayed myelination. Clin Dysmorphol 2022; 31:196-200. [PMID: 35445667 PMCID: PMC9474726 DOI: 10.1097/mcd.0000000000000423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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10
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Moreno Traspas R, Teoh TS, Wong PM, Maier M, Chia CY, Lay K, Ali NA, Larson A, Al Mutairi F, Al-Sannaa NA, Faqeih EA, Alfadhel M, Cheema HA, Dupont J, Bézieau S, Isidor B, Low DY, Wang Y, Tan G, Lai PS, Piloquet H, Joubert M, Kayserili H, Kripps KA, Nahas SA, Wartchow EP, Warren M, Bhavani GS, Dasouki M, Sandoval R, Carvalho E, Ramos L, Porta G, Wu B, Lashkari HP, AlSaleem B, BaAbbad RM, Abreu Ferrão AN, Karageorgou V, Ordonez-Herrera N, Khan S, Bauer P, Cogne B, Bertoli-Avella AM, Vincent M, Girisha KM, Reversade B. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nat Genet 2022; 54:1214-1226. [PMID: 35864190 PMCID: PMC7615854 DOI: 10.1038/s41588-022-01120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient's primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.
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Affiliation(s)
- Ricardo Moreno Traspas
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze Shin Teoh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Michael Maier
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Nur Ain Ali
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Austin Larson
- Section of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Fuad Al Mutairi
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Medical Genomic Research, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Huma Arshad Cheema
- Division of Pediatric Gastroenterology-Hepatology and Nutrition, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Juliette Dupont
- Department of Pediatrics, Genetic Services, Lisbon North University Hospital Center, Lisbon, Portugal
| | - Stéphane Bézieau
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Dorrain Yanwen Low
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Grace Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hugues Piloquet
- Gastropediatrics Department, Nantes University Hospital Center, Nantes, France
| | - Madeleine Joubert
- Anatomopathology Department, Nantes University Hospital Center, Nantes, France
| | - Hulya Kayserili
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric P Wartchow
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Majed Dasouki
- Department of Pediatric Genetics, AdventHealth Medical Group, Orlando, FL, USA
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sírio-Libanês, Brasília, Brazil
| | - Elisa Carvalho
- Department of Pediatric Gastroenterology and Hepatology, Hospital da Criança de Brasília José Alencar, UniCEUB, Brasília, Brazil
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | - Gilda Porta
- Department of Pediatric Hepatology, Transplant Unit, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Badr AlSaleem
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raeda M BaAbbad
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Benjamin Cogne
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Marie Vincent
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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11
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Juneja M, Gupta A, Sairam S, Jain R, Sharma M, Thadani A, Srinivasan R, Lingappa L, Ahmed S, Multani KS, Buch P, Chatterjee N, Dalwai S, Kabra M, Kapoor S, Patel PK, Girisha KM, Kulkarni M, Kunju PAM, Malhi P, Meenai Z, Mishra D, Mundkur N, Nair MKC, Oommen SP, Prasad C, Singh A, Srivastava L, Suman P, Thakur R. Diagnosis and Management of Global Development Delay: Consensus Guidelines of Growth, Development and Behavioral Pediatrics Chapter, Neurology Chapter and Neurodevelopment Pediatrics Chapter of the Indian Academy of Pediatrics. Indian Pediatr 2022; 59:401-415. [PMID: 35188106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
JUSTIFICATION Global developmental delay (GDD) is a relatively common neurodevelopmental disorder; however, paucity of published literature and absence of uniform guidelines increases the complexity of clinical management of this condition. Hence, there is a need of practical guidelines for the pediatrician on the diagnosis and management of GDD, summarizing the available evidence, and filling in the gaps in existing knowledge and practices. PROCESS Seven subcommittees of subject experts comprising of writing and expert group from among members of Indian Academy of Pediatrics (IAP) and its chapters of Neurology, Neurodevelopment Pediatrics and Growth Development and Behavioral Pediatrics were constituted, who reviewed literature, developed key questions and prepared the first draft on guidelines after multiple rounds of discussion. The guidelines were then discussed by the whole group in an online meeting. The points of contention were discussed and a general consensus was arrived at, after which final guidelines were drafted by the writing group and approved by all contributors. The guidelines were then approved by the Executive Board of IAP. Guidelines GDD is defined as significant delay (at least 2 standard deviations below the mean with standardized developmental tests) in at least two developmental domains in children under 5 years of age; however, children whose delay can be explained primarily by motor issues or severe uncorrected visual/hearing impairment are excluded. Severity of GDD can be classified as mild, moderate, severe and profound on adaptive functioning. For all children, in addition to routine surveillance, developmental screening using standardized tools should be done at 9-12 months,18-24 months, and at school entry; whereas, for high risk infants, it should be done 6-monthly till 24 months and yearly till 5 years of age; in addition to once at school entry. All children, especially those diagnosed with GDD, should be screened for ASD at 18-24 months, and if screen negative, again at 3 years of age. It is recommended that investigations should always follow a careful history and examination to plan targeted testing and, vision and hearing screening should be done in all cases prior to standardized tests of development. Neuro-imaging, preferably magnetic resonance imaging of the brain, should be obtained when specific clinical indicators are present. Biochemical and metabolic investigations should be targeted towards identifying treatable conditions and genetic tests are recommended in presence of clinical suspicion of a genetic syndrome and/or in the absence of a clear etiology. Multidisciplinary intervention should be initiated soon after the delay is recognized even before a formal diagnosis is made, and early intervention for high risk infants should start in the nursery with developmentally supportive care. Detailed structured counselling of family regarding the diagnosis, etiology, comorbidities, investigations, management, prognosis and follow-up is recommended. Regular targeted follow-up should be done, preferably in consultation with a team of experts led by a developmental pediatrician/ pediatric neurologist.
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Affiliation(s)
- Monica Juneja
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi. Correspondence to: Dr Monica Juneja, Director-Professor and Head, Department of Pediatrics, Maulana Azad Medical College, New Delhi.
| | - Arpita Gupta
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi
| | - Smitha Sairam
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi
| | - Ridhimaa Jain
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi
| | - Monika Sharma
- Department of Pediatrics, Christian Medical College, Ludhiana
| | - Anjana Thadani
- Niramaya Hospital and Guidance Clinic, Chembur, Mumbai, Maharashtra
| | | | | | - Shabina Ahmed
- Indian Academy of Pediatrics, Neurodevelopment Chapter
| | - K S Multani
- Indian Academy of Pediatrics, Neurodevelopment Chapter
| | - Pankaj Buch
- Department of Pediatrics, MP Shah Government Medical College, Jamnagar, Gujarat
| | | | - Samir Dalwai
- New Horizons Child Development Centre, Mumbai, Maharashtra
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), New Delhi
| | - Seema Kapoor
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi
| | | | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Karnataka
| | | | - P A M Kunju
- Department of Pediatric Neurology, Medical College Thiruvananthapuram, Kerala
| | - Prahbhjot Malhi
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh
| | - Zafar Meenai
- Ummeid Group of Child Development Centers, Bhopal, Madhya Pradesh
| | - Devendra Mishra
- Department of Pediatrics, Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi
| | - Nandini Mundkur
- Center for Child Development and Disabilities (CCDD) Bengaluru, Karnataka
| | - M K C Nair
- NIMS-SPECTRUM-Child Development Research Centre (CDRC) NIMS Medicity, Thiruvananthapuram, Kerala
| | | | - Chhaya Prasad
- ASHA, Centre for Autism and Intellectual Developmental Disorders, Chandigarh
| | - Arun Singh
- All India Institute of Medical Sciences, Jodhpur, Rajasthan
| | - Leena Srivastava
- Bharati Vidyapeeth Medical College and Hospital, Pune, Maharashtra
| | - Praveen Suman
- Child Development Centre, Sir Gangaram Hospital, New Delhi
| | - Rahul Thakur
- The Children's Neurodevelopmental Centre, Patna, Bihar
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12
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Vona B, Schwartzbaum DA, Rodriguez AA, Lewis SS, Toosi MB, Radhakrishnan P, Bozan N, Akın R, Doosti M, Manju R, Duman D, Sineni CJ, Nampoothiri S, Karimiani EG, Houlden H, Bademci G, Tekin M, Girisha KM, Maroofian R, Douzgou S. Biallelic KITLG variants lead to a distinct spectrum of hypomelanosis and sensorineural hearing loss. J Eur Acad Dermatol Venereol 2022; 36:1606-1611. [PMID: 35543077 PMCID: PMC9546089 DOI: 10.1111/jdv.18207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/21/2022] [Indexed: 11/30/2022]
Abstract
Background Pathogenic variants in KITLG, a crucial protein involved in pigmentation and neural crest cell migration, cause non‐syndromic hearing loss, Waardenburg syndrome type 2, familial progressive hyperpigmentation and familial progressive hyper‐ and hypopigmentation, all of which are inherited in an autosomal dominant manner. Objectives To describe the genotypic and clinical spectrum of biallelic KITLG‐variants. Methods We used a genotype‐first approach through the GeneMatcher data sharing platform to collect individuals with biallelic KITLG variants and reviewed the literature for overlapping reports. Results We describe the first case series with biallelic KITLG variants; we expand the known hypomelanosis spectrum to include a ‘sock‐and‐glove‐like’, symmetric distribution, progressive repigmentation and generalized hypomelanosis. We speculate that KITLG biallelic loss‐of‐function variants cause generalized hypomelanosis, whilst variants with residual function lead to a variable auditory‐pigmentary disorder mostly reminiscent of Waardenburg syndrome type 2 or piebaldism. Conclusions We provide consolidating evidence that biallelic KITLG variants cause a distinct auditory‐pigmentary disorder. We evidence a significant clinical variability, similar to the one previously observed in KIT‐related piebaldism.
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Affiliation(s)
- B Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - D A Schwartzbaum
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - A A Rodriguez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - S S Lewis
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - M B Toosi
- Department of Pediatrics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - P Radhakrishnan
- Suma Genomics Private Limited and Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - N Bozan
- Department of Otolaryngology, Yuzuncu Yıl University Faculty of Medicine, Van, Turkey
| | - R Akın
- Department of Otolaryngology, Yuzuncu Yıl University Faculty of Medicine, Van, Turkey
| | - M Doosti
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - R Manju
- Renai Medicity, Cochin, Kerala, India
| | - D Duman
- Department of Audiology, Ankara University Faculty of Health Sciences, Ankara, Turkey
| | - C J Sineni
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - S Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, India
| | - E G Karimiani
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran.,Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.,Innovative medical research center, Mashhad branch, Islamic Azad University, Mashhad, Iran
| | - H Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - G Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.,Suma Genomics Private Limited and Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | - R Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - S Douzgou
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
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13
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Holling T, Nampoothiri S, Tarhan B, Schneeberger PE, Vinayan KP, Yesodharan D, Roy AG, Radhakrishnan P, Alawi M, Rhodes L, Girisha KM, Kang PB, Kutsche K. Novel biallelic variants expand the SLC5A6-related phenotypic spectrum. Eur J Hum Genet 2022; 30:439-449. [PMID: 35013551 PMCID: PMC8747999 DOI: 10.1038/s41431-021-01033-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
The sodium (Na+):multivitamin transporter (SMVT), encoded by SLC5A6, belongs to the sodium:solute symporter family and is required for the Na+-dependent uptake of biotin (vitamin B7), pantothenic acid (vitamin B5), the vitamin-like substance α-lipoic acid, and iodide. Compound heterozygous SLC5A6 variants have been reported in individuals with variable multisystemic disorder, including failure to thrive, developmental delay, seizures, cerebral palsy, brain atrophy, gastrointestinal problems, immunodeficiency, and/or osteopenia. We expand the phenotypic spectrum associated with biallelic SLC5A6 variants affecting function by reporting five individuals from three families with motor neuropathies. We identified the homozygous variant c.1285 A > G [p.(Ser429Gly)] in three affected siblings and a simplex patient and the maternally inherited c.280 C > T [p.(Arg94*)] variant and the paternally inherited c.485 A > G [p.(Tyr162Cys)] variant in the simplex patient of the third family. Both missense variants were predicted to affect function by in silico tools. 3D homology modeling of the human SMVT revealed 13 transmembrane helices (TMs) and Tyr162 and Ser429 to be located at the cytoplasmic facing region of TM4 and within TM11, respectively. The SLC5A6 missense variants p.(Tyr162Cys) and p.(Ser429Gly) did not affect plasma membrane localization of the ectopically expressed multivitamin transporter suggesting reduced but not abolished function, such as lower catalytic activity. Targeted therapeutic intervention yielded clinical improvement in four of the five patients. Early molecular diagnosis by exome sequencing is essential for timely replacement therapy in affected individuals.
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Bedirhan Tarhan
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Pauline E Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Amedes MVZ Wagnerstibbe für Laboratoriumsmedizin, Hämostaseologie, Humangenetik und Mikrobiologie Hannover, 30159, Hannover, Germany
| | | | - Dhanya Yesodharan
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Arun Grace Roy
- Department of Neurology, Amrita Institute of Medical Sciences & Research Centre, Cochin, 682041, Kerala, India
| | - Periyasamy Radhakrishnan
- Suma Genomics Pvt. Ltd, Manipal Universal Technology Business Incubator (MUTBI), Manipal, 576104, India
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, 576104, India
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, 32610, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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14
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Holling T, Bhavani GS, von Elsner L, Shah H, Kausthubham N, Bhattacharyya SS, Shukla A, Mortier GR, Schinke T, Danyukova T, Pohl S, Kutsche K, Girisha KM. A homozygous hypomorphic BNIP1 variant causes an increase in autophagosomes and reduced autophagic flux and results in a spondylo-epiphyseal dysplasia. Hum Mutat 2022; 43:625-642. [PMID: 35266227 DOI: 10.1002/humu.24368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 01/18/2023]
Abstract
BNIP1 (BCL2 interacting protein 1) is a soluble N-ethylmaleimide-sensitive factor-attachment protein receptor involved in ER membrane fusion. We identified the homozygous BNIP1 intronic variant c.84+3A>T in the apparently unrelated patients 1 and 2 with disproportionate short stature. Radiographs showed abnormalities affecting both the axial and appendicular skeleton and spondylo-epiphyseal dysplasia. We detected ~80% aberrantly spliced BNIP1 pre-mRNAs, reduced BNIP1 mRNA level to ~80%, and BNIP1 protein level reduction by ~50% in patient 1 compared to control fibroblasts. The BNIP1 ortholog in drosophila, Sec. 20, regulates autophagy and lysosomal degradation. We assessed lysosome positioning and identified a decrease in lysosomes in the perinuclear region and an increase in the cell periphery in patient 1 cells. Immunofluorescence microscopy and immunoblotting demonstrated an increase in LC3B-positive structures and LC3B-II levels, respectively, in patient 1 fibroblasts under steady-state condition. Treatment of serum-starved fibroblasts with or without bafilomycin A1 identified significantly decreased autophagic flux in patient 1 cells. Our data suggest a block at the terminal stage of autolysosome formation and/or clearance in patient fibroblasts. BNIP1 together with RAB33B and VPS16, disease genes for Smith-McCort dysplasia 2 and a multisystem disorder with short stature, respectively, highlight the importance of autophagy in skeletal development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hitesh Shah
- Department of Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Geert R Mortier
- Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatyana Danyukova
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Pohl
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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15
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Klöckner C, Murray JPF, Tavasoli M, Sticht H, Stoltenburg-Didinger G, Scholle LM, Bakhtiari S, Kruer MC, Darvish H, Firouzabadi SG, Pagnozzi A, Shukla A, Girisha KM, Narayanan DL, Kaur P, Maroofian R, Zaki MS, Noureldeen MM, Merkenschlager A, Gburek-Augustat J, Cali E, Banu S, Nahar K, Efthymiou S, Houlden H, Jamra RA, Williams J, McMaster CR, Platzer K. Bi-allelic variants in CHKA cause a neurodevelopmental disorder with epilepsy and microcephaly. Brain 2022; 145:1916-1923. [PMID: 35202461 DOI: 10.1093/brain/awac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/15/2021] [Accepted: 02/06/2022] [Indexed: 11/14/2022] Open
Abstract
The Kennedy pathways catalyze the de novo synthesis of phosphatidylcholine and phosphatidylethanolamine, the most abundant components of eukaryotic cell membranes. In recent years, these pathways have moved into clinical focus since four out of ten genes involved have been associated with a range of autosomal recessive rare diseases such as a neurodevelopmental disorder with muscular dystrophy (CHKB), bone abnormalities and cone-rod dystrophy (PCYT1A), and spastic paraplegia (PCYT2, SELENOI). We identified six individuals from five families with bi-allelic variants in CHKA presenting with severe global developmental delay, epilepsy, movement disorders, and microcephaly. Using structural molecular modeling and functional testing of the variants in a in a cell-based S. cerevisiae model, we determined that these variants reduce the enzymatic activity of CHKA and confer a significant impairment of the first enzymatic step of the Kennedy pathway. In summary, we present CHKA as a novel autosomal recessive gene for a neurodevelopmental disorder with epilepsy and microcephaly.
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Affiliation(s)
- Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Mahtab Tavasoli
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3N 0A1, Canada
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA.,Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA.,Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane, QLD 4029, Australia
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mahmoud M Noureldeen
- Department of Pediatrics, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Andreas Merkenschlager
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University Hospital Leipzig, Leipzig, Germany
| | - Janina Gburek-Augustat
- Division of Neuropaediatrics, Hospital for Children and Adolescents, University Hospital Leipzig, Leipzig, Germany
| | - Elisa Cali
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Selina Banu
- Department of Pediatric Neurology, Dr. M.R. Khan Shishu (Children) Hospital and ICH, Mirpur, Dhaka, Bangladesh
| | - Kamrun Nahar
- Department of Pediatric Neurology, Dr. M.R. Khan Shishu (Children) Hospital and ICH, Mirpur, Dhaka, Bangladesh
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Jason Williams
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3N 0A1, Canada
| | | | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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16
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Altunoglu U, Börklü E, Shukla A, Escande-Beillard N, Ledig S, Azaklı H, Nayak SS, Eraslan S, Girisha KM, Kennerknecht I, Kayserili H. Expanding the spectrum of syndromic PPP2R3C-related XY gonadal dysgenesis to XX gonadal dysgenesis. Clin Genet 2021; 101:221-232. [PMID: 34750818 DOI: 10.1111/cge.14086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 01/09/2023]
Abstract
Homozygous variants in PPP2R3C have been reported to cause a syndromic 46,XY complete gonadal dysgenesis phenotype with extragonadal manifestations (GDRM, MIM# 618419) in patients from four unrelated families, whereas heterozygous variants have been linked to reduced fertility with teratozoospermia (SPGF36, MIM# 618420) in male carriers. We present eight patients from four unrelated families of Turkish and Indian descent with three different germline homozygous PPP2R3C variants including a novel in-frame duplication (c.639_647dupTTTCTACTC, p.Ser216_Tyr218dup). All patients exhibit recognizable facial dysmorphisms allowing gestalt diagnosis. In two 46,XX patients with hypergonadotropic hypogonadism and nonvisualized gonads, primary amenorrhea along with absence of secondary sexual characteristics and/or unique facial gestalt led to the diagnosis. 46,XY affected individuals displayed a spectrum of external genital phenotypes from ambiguous genitalia to complete female. We expand the spectrum of syndromic PPP2R3C-related XY gonadal dysgenesis to both XY and XX gonadal dysgenesis. Our findings supported neither ocular nor muscular involvement as major criteria of the syndrome. We also did not encounter infertility problems in the carriers. Since both XX and XY individuals were affected, we hypothesize that PPP2R3C is essential in the early signaling cascades controlling sex determination in humans.
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Affiliation(s)
- Umut Altunoglu
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey.,Medical Genetics Department, Istanbul University Istanbul Medical School, Istanbul, Turkey
| | - Esra Börklü
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Nathalie Escande-Beillard
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey.,Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Susanne Ledig
- Institut für Humangenetik, Westfaelische Wilhelms-Universitaet Muenster, Muenster, Germany
| | - Hülya Azaklı
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Serpil Eraslan
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ingo Kennerknecht
- Institut für Humangenetik, Westfaelische Wilhelms-Universitaet Muenster, Muenster, Germany
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSoM) and Hospital, Istanbul, Turkey.,Medical Genetics Department, Istanbul University Istanbul Medical School, Istanbul, Turkey
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17
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Narayanan DL, Girisha KM. Understanding Exome Sequencing: Tips for the Pediatrician. Indian Pediatr 2021; 58:771-774. [PMID: 33634792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Exome sequencing is gaining popularity as a genomic test for the diagnosis of Mendelian disorders in children. It is essential for pediatricians to familiarize themselves with this technique and its interpretation. This brief review discusses some of the key components of a clinical or research report on exome sequencing for a practicing pediatrician, so as to enable them to utilize this test well and provide timely referrals to a clinical geneticist.
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Affiliation(s)
- Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, (Manipal Academy of Higher Education), Manipal, India. Correspondence to: Dr Girisha KM, Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576 104.
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18
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Narayanan DL, Girisha KM. Understanding Exome Sequencing: Tips for the Pediatrician. Indian Pediatr 2021. [DOI: 10.1007/s13312-021-2289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Majethia P, Somashekar PH, Hebbar M, Kadavigere R, Praveen BK, Girisha KM, Shukla A. Biallelic start loss variant, c.1A > G in GCSH is associated with variant nonketotic hyperglycinemia. Clin Genet 2021; 100:201-205. [PMID: 33890291 PMCID: PMC9990824 DOI: 10.1111/cge.13970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
The glycine cleavage system H protein (GCSH) is an integral part of the glycine cleavage system with its additional involvement in the synthesis and transport of lipoic acid. We hypothesize that pathogenic variants in GCSH can cause variant nonketotic hyperglycinemia (NKH), a heterogeneous group of disorders with findings resembling a combination of severe NKH (elevated levels of glycine in plasma and CSF, progressive lethargy, seizures, severe hypotonia, no developmental progress, early death) and mitochondriopathies (lactic acidosis, leukoencephalopathy and Leigh-like lesions on MRI). We herein report three individuals from two unrelated Indian families with clinical, biochemical, and radiological findings of variant NKH, harboring a biallelic start loss variant, c.1A > G in GCSH.
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Affiliation(s)
- Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - BK Praveen
- Department of Pediatrics, Father Muller Medical College Hospital, Mangalore, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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20
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Kaur P, do Rosario MC, Hebbar M, Sharma S, Kausthubham N, Nair K, A S, Bhat Y R, Lewis LES, Nampoothiri S, Patil SJ, Suresh N, Bijarnia Mahay S, Dua Puri R, Pai S, Kaur A, Kc R, Kamath N, Bajaj S, Kumble A, Shetty R, Shenoy R, Kamate M, Shah H, Muranjan MN, Bl Y, Avabratha KS, Subramaniam G, Kadavigere R, Bielas S, Girisha KM, Shukla A. Clinical and genetic spectrum of 104 Indian families with central nervous system white matter abnormalities. Clin Genet 2021; 100:542-550. [PMID: 34302356 PMCID: PMC8918360 DOI: 10.1111/cge.14037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022]
Abstract
Genetic disorders with predominant central nervous system white matter abnormalities (CNS WMAs), also called leukodystrophies, are heterogeneous entities. We ascertained 117 individuals with CNS WMAs from 104 unrelated families. Targeted genetic testing was carried out in 16 families and 13 of them received a diagnosis. Chromosomal microarray (CMA) was performed for three families and one received a diagnosis. Mendeliome sequencing was used for testing 11 families and all received a diagnosis. Whole exome sequencing (WES) was performed in 80 families and was diagnostic in 52 (65%). Singleton WES was diagnostic for 50/75 (66.67%) families. Overall, genetic diagnoses were obtained in 77 families (74.03%). Twenty-two of 47 distinct disorders observed in this cohort have not been reported in Indian individuals previously. Notably, disorders of nuclear mitochondrial pathology were most frequent (9 disorders in 20 families). Thirty-seven of 75 (49.33%) disease-causing variants are novel. To sum up, the present cohort describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It demonstrates WES, especially singleton WES, as an efficient tool in the diagnosis of these heterogeneous entities. It also highlights possible founder events and recurrent disease-causing variants in our population and their implications on the testing strategy.
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Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karthik Nair
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shrikiran A
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ramesh Bhat Y
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Leslie Edward S Lewis
- Department of Paediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Kochi, India
| | | | - Narayanaswami Suresh
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Shivanand Pai
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Anupriya Kaur
- Department of Paediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakshith Kc
- Department of Neurology, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Nutan Kamath
- Department of Paediatrics, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Bajaj
- Jaslok Hospital and Research Centre, Mumbai, India
| | - Ali Kumble
- Department of Paediatrics, Indiana Hospital and Heart Institute, Mangalore, India
| | | | - Rathika Shenoy
- Department of Paediatrics, K.S. Hegde Medical Academy, NITTE University, Mangalore, India
| | - Mahesh Kamate
- Department of Paediatrics, Jawaharlal Nehru Medical College, Belgaum, India
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mamta N Muranjan
- Department of Pediatrics, Genetics Division, Seth Gordhandas Sunderdas Medical College and King Edward VII Memorial Hospital, Mumbai, Maharashtra, India
| | - Yatheesha Bl
- Dheemahi Child Neurology and Development Center, Shimoga, India
| | | | | | - Rajagopal Kadavigere
- Department of Radiodiagnosis, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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21
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Narayanan DL, Udyawar D, Kaur P, Sharma S, Suresh N, Nampoothiri S, do Rosario MC, Somashekar PH, Rao LP, Kausthubham N, Majethia P, Pande S, Ramesh Bhat Y, Shrikiran A, Bielas S, Girisha KM, Shukla A. Multilocus disease-causing genomic variations for Mendelian disorders: role of systematic phenotyping and implications on genetic counselling. Eur J Hum Genet 2021; 29:1774-1780. [PMID: 34276053 PMCID: PMC8633282 DOI: 10.1038/s41431-021-00933-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/24/2021] [Accepted: 06/22/2021] [Indexed: 11/09/2022] Open
Abstract
Multilocus disease-causing genomic variations (MGVs) and multiple genetic diagnoses (MGDs) are increasingly being recognised in individuals and families with Mendelian disorders. This can be mainly attributed to the widespread use of genomic tests for the evaluation of these disorders. We conducted a retrospective study of families evaluated over the last 6 years at our centre to identify families with MGVs and MGDs. MGVs were observed in fourteen families. We observed five different consequences: (i) individuals with MGVs presenting as blended phenotypes (ii) individuals with MGVs presenting with distinct phenotypes (iii) individuals with MGVs with age-dependent penetrance (iv) individuals with MGVs with one phenotype obscured by another more predominant phenotype (v) two distinct phenotypes in different individuals in families with MGVs. Consanguinity was present in eight (8/14, 57.1%) of them. Thirteen families had two Mendelian disorders and one had three Mendelian disorders. The risk of recurrence of one or more conditions in these families ranged from 25% to 75%. Our findings underline the importance of the role of a clinical geneticist in systematic phenotyping, challenges in genetic counselling and risk estimation in families with MGVs and MGDs, especially in highly inbred populations.
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Affiliation(s)
- Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Divya Udyawar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Department of Pediatrics (Neurology division), Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Narayanaswamy Suresh
- Department of Pediatrics (Neurology division), Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Y Ramesh Bhat
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Aroor Shrikiran
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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22
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Somashekar PH, Kaur P, Stephen J, Guleria VS, Kadavigere R, Girisha KM, Bielas S, Upadhyai P, Shukla A. Bi-allelic missense variant, p.Ser35Leu in EXOSC1 is associated with pontocerebellar hypoplasia. Clin Genet 2021; 99:594-600. [PMID: 33463720 PMCID: PMC9990822 DOI: 10.1111/cge.13928] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
RNA exosome is a highly conserved ribonuclease complex essential for RNA processing and degradation. Bi-allelic variants in exosome subunits EXOSC3, EXOSC8 and EXOSC9 have been reported to cause pontocerebellar hypoplasia type 1B, type 1C and type 1D, respectively, while those in EXOSC2 cause short stature, hearing loss, retinitis pigmentosa and distinctive facies. We ascertained an 8-months-old male with developmental delay, microcephaly, subtle dysmorphism and hypotonia. Pontocerebellar hypoplasia and delayed myelination were noted on neuroimaging. A similarly affected elder sibling succumbed at the age of 4-years 6-months. Chromosomal microarray returned normal results. Exome sequencing revealed a homozygous missense variant, c.104C > T p.(Ser35Leu) in EXOSC1 (NM_016046.5) as the possible candidate. In silico mutagenesis revealed loss of a polar contact with neighboring Leu37 residue. Quantitative real-time PCR indicated no appreciable differences in EXOSC1 transcript levels. Immunoblotting and blue native PAGE revealed reduction in the EXOSC1 protein levels and EXO9 complex in the proband, respectively. We herein report an individual with the bi-allelic variant c.104C>T p.(Ser35Leu) in EXOSC1 and clinical features of pontocerebellar hypoplasia type 1. Immunoblotting and blue native PAGE provide evidence for the pathogenicity of the variant. Thus, we propose EXOSC1 as a novel candidate gene for pontocerebellar hypoplasia.
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Affiliation(s)
- Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Joshi Stephen
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vishal Singh Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Majethia P, Girisha KM. Wiedemann-Rautenstrauch syndrome in an Indian patient with biallelic pathogenic variants in POLR3A. Am J Med Genet A 2021; 185:1602-1605. [PMID: 33559318 DOI: 10.1002/ajmg.a.62115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/02/2021] [Accepted: 01/12/2021] [Indexed: 11/11/2022]
Abstract
Wiedemann-Rautenstrauch syndrome (WRS; MIM# 264090) is a rare neonatal progeroid disorder resulting from biallelic pathogenic variants in the POLR3A. It is an autosomal recessive condition characterized by growth retardation, lipoatrophy, a distinctive face, sparse scalp hair, and dental anomalies. Till date, 19 families are reported with WRS due to variants in POLR3A. Here, we describe an 18 months old male child with biallelic c.2005C>T p.(Arg669Ter) and c.1771-7C>G variant in heterozygous state identified by exome sequencing in POLR3A leading to WRS phenotype. The variant c.1771-7C>G was earlier found to be associated with hereditary spastic ataxia. We emphasize on the phenotype in an Indian patient with WRS.
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Affiliation(s)
- Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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24
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Sheikh TI, Vasli N, Pastore S, Kharizi K, Harripaul R, Fattahi Z, Pande S, Naeem F, Hussain A, Mir A, Islam O, Girisha KM, Irfan M, Ayub M, Schwarzer C, Najmabadi H, Shukla A, Sladky VC, Braun VZ, Garcia-Carpio I, Villunger A, Vincent JB. Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability. Transl Psychiatry 2021; 11:1. [DOI: https:/doi.org/10.1038/s41398-020-01158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 10/10/2023] Open
Abstract
AbstractPIDD1 encodes p53-Induced Death Domain protein 1, which acts as a sensor surveilling centrosome numbers and p53 activity in mammalian cells. Early results also suggest a role in DNA damage response where PIDD1 may act as a cell-fate switch, through interaction with RIP1 and NEMO/IKKg, activating NF-κB signaling for survival, or as an apoptosis-inducing protein by activating caspase-2. Biallelic truncating mutations in CRADD—the protein bridging PIDD1 and caspase-2—have been reported in intellectual disability (ID), and in a form of lissencephaly. Here, we identified five families with ID from Iran, Pakistan, and India, with four different biallelic mutations in PIDD1, all disrupting the Death Domain (DD), through which PIDD1 interacts with CRADD or RIP1. Nonsense mutations Gln863* and Arg637* directly disrupt the DD, as does a missense mutation, Arg815Trp. A homozygous splice mutation in the fifth family is predicted to disrupt splicing upstream of the DD, as confirmed using an exon trap. In HEK293 cells, we show that both Gln863* and Arg815Trp mutants fail to co-localize with CRADD, leading to its aggregation and mis-localization, and fail to co-precipitate CRADD. Using genome-edited cell lines, we show that these three PIDD1 mutations all cause loss of PIDDosome function. Pidd1 null mice show decreased anxiety, but no motor abnormalities. Together this indicates that PIDD1 mutations in humans may cause ID (and possibly lissencephaly) either through gain of function or secondarily, due to altered scaffolding properties, while complete loss of PIDD1, as modeled in mice, may be well tolerated or is compensated for.
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25
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Sheikh TI, Vasli N, Pastore S, Kharizi K, Harripaul R, Fattahi Z, Pande S, Naeem F, Hussain A, Mir A, Islam O, Girisha KM, Irfan M, Ayub M, Schwarzer C, Najmabadi H, Shukla A, Sladky VC, Braun VZ, Garcia-Carpio I, Villunger A, Vincent JB. Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability. Transl Psychiatry 2021; 11:1. [PMID: 33414379 PMCID: PMC7791037 DOI: 10.1038/s41398-020-01158-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
PIDD1 encodes p53-Induced Death Domain protein 1, which acts as a sensor surveilling centrosome numbers and p53 activity in mammalian cells. Early results also suggest a role in DNA damage response where PIDD1 may act as a cell-fate switch, through interaction with RIP1 and NEMO/IKKg, activating NF-κB signaling for survival, or as an apoptosis-inducing protein by activating caspase-2. Biallelic truncating mutations in CRADD-the protein bridging PIDD1 and caspase-2-have been reported in intellectual disability (ID), and in a form of lissencephaly. Here, we identified five families with ID from Iran, Pakistan, and India, with four different biallelic mutations in PIDD1, all disrupting the Death Domain (DD), through which PIDD1 interacts with CRADD or RIP1. Nonsense mutations Gln863* and Arg637* directly disrupt the DD, as does a missense mutation, Arg815Trp. A homozygous splice mutation in the fifth family is predicted to disrupt splicing upstream of the DD, as confirmed using an exon trap. In HEK293 cells, we show that both Gln863* and Arg815Trp mutants fail to co-localize with CRADD, leading to its aggregation and mis-localization, and fail to co-precipitate CRADD. Using genome-edited cell lines, we show that these three PIDD1 mutations all cause loss of PIDDosome function. Pidd1 null mice show decreased anxiety, but no motor abnormalities. Together this indicates that PIDD1 mutations in humans may cause ID (and possibly lissencephaly) either through gain of function or secondarily, due to altered scaffolding properties, while complete loss of PIDD1, as modeled in mice, may be well tolerated or is compensated for.
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Affiliation(s)
- Taimoor I Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Molecular Genetics Laboratory, North York General Hosptial Genetics Program, Toronto, ON, M2K 1E1, Canada
| | - Nasim Vasli
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Stephen Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Kimia Kharizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
| | - Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Farooq Naeem
- General and Health Systems Psychiatry, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Abrar Hussain
- Human Molecular Genetics Lab, Department of Biological Sciences, FBAS, International Islamic University, Islamabad, Pakistan
| | - Asif Mir
- Human Molecular Genetics Lab, Department of Biological Sciences, FBAS, International Islamic University, Islamabad, Pakistan
| | - Omar Islam
- Department of Diagnostic Radiology, Queens University, Kingston, ON, K7L 2V7, Canada
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Muhammad Irfan
- Department of Mental Health, Psychiatry and Behavioural Sciences, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Muhammad Ayub
- Lahore Institute of Research & Development, Lahore, 51000, Pakistan
- Department of Psychiatry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, 14667, Iran
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Valentina C Sladky
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Vincent Zoran Braun
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Irmina Garcia-Carpio
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria.
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada.
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Mishra S, Girisha KM, Shukla A. Expanding the phenotype of PURA-related neurodevelopmental disorder: a close differential diagnosis of infantile hypotonia with psychomotor retardation and characteristic facies. Clin Dysmorphol 2021; 30:1-5. [PMID: 33229923 PMCID: PMC9944571 DOI: 10.1097/mcd.0000000000000360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Purine-rich element-binding protein A (PURA) encodes Pur-alpha, a transcriptional activator protein is crucial for normal brain development. Pathogenic variants in PURA are known to cause mental retardation, autosomal dominant 31, characterized by psychomotor delay, absent or poor speech, hypotonia, feeding difficulties, seizures or 'seizure-like' movements, and dysmorphism. PURA-related neurodevelopmental disorder (PURA-related NDD) result either from heterozygous pathogenic sequence variants in PURA or microdeletions spanning PURA. Singleton whole-exome sequencing (WES) was performed for the proband after a clinical diagnosis of infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF) was made. The pathogenic variant was validated by Sanger sequencing in the proband and parents. Comparison of PURA-related NDD and IHPRF was carried out. WES identified a novel, de-novo stop-gain variant c.178G>T in PURA. In addition to typical phenotype, subject also had hypersensitivity to various stimuli which was not reported in PURA-related NDD. Significant phenotypic overlap was observed in subjects with PURA-related NDD and IHPRF especially with IHPRF2, caused by biallelic pathogenic variants in UNC80. This study expands the phenotypic and mutational spectrum of PURA-related NDD. We propose PURA-related NDD to be considered as a close differential diagnosis of IHPRF.
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Affiliation(s)
- Shivani Mishra
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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Shukla A, Kaur P, Narayanan DL, do Rosario MC, Kadavigere R, Girisha KM. Genetic disorders with central nervous system white matter abnormalities: An update. Clin Genet 2021; 99:119-132. [PMID: 33047326 PMCID: PMC9951823 DOI: 10.1111/cge.13863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/21/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
Several genetic disorders have variable degree of central nervous system white matter abnormalities. We retrieved and reviewed 422 genetic conditions with prominent and consistent involvement of white matter from the literature. We herein describe the current definitions, classification systems, clinical spectrum, neuroimaging findings, genomics, and molecular mechanisms of these conditions. Though diagnosis for most of these disorders relies mainly on genomic tests, specifically exome sequencing, we collate several clinical and neuroimaging findings still relevant in diagnosis of clinically recognizable disorders. We also review the current understanding of pathophysiology and therapeutics of these disorders.
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Affiliation(s)
- Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Patil SJ, Pande S, Matalia J, Bhat V, Kekatpure M, Girisha KM. Knobloch Syndrome in Siblings with Posterior Fossa Malformations Along with Cerebellar Midline Cleft Abnormality Caused by Biallelic COL18A1 Mutation: Case-Based Review. J Pediatr Genet 2020; 12:58-63. [PMID: 36684549 PMCID: PMC9848758 DOI: 10.1055/s-0040-1721073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/11/2020] [Indexed: 01/25/2023]
Abstract
Knobloch syndrome (KS) is an autosomal recessive disorder caused by biallelic pathogenic variants in COL18A1 . KS clinically manifests with the typical eye findings (high myopia, vitreoretinal degeneration, retinal detachment, and lens subluxation), variable neurological findings (occipital encephalocele, polymicrogyria, cerebellar malformations, epilepsy, and intellectual disability), and the other uncommon clinical manifestations. Literature review of all KS patients (source PubMed) was done with special reference to cerebellar abnormalities. Here, we report two siblings with typical KS with posterior fossa malformations and novel cerebellar midline cleft abnormality analyzed by whole exome sequencing. Known pathogenic homozygous variant c.2908C > T; (p.Arg970Ter) in exon 26 of COL18A1 was found as a cause for KS. These two siblings presented with early-onset severe ocular manifestations, facial dysmorphism, and variable central nervous system manifestations along with novel cerebellar midline cleft abnormality. The presence or absence of structural brain malformations and genotypes does not absolutely predict cognitive functions in KS patients. However, the presence of posterior fossa abnormality may be predictive for the development of ataxia in later life and needs further studies.
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Affiliation(s)
- Siddaramappa J. Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India,Address for correspondence Siddaramappa J. Patil, MD (Ped), DM (Medical Genetics) Mazumdar Shaw Medical Centre, Narayana Hrudayalaya HospitalsNo 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore 560099India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Jyoti Matalia
- Department of Pediatric Ophthalmology and Strabismology, Narayana Nethralaya, Bangalore, India
| | - Venkatraman Bhat
- Department of Radiology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Minal Kekatpure
- Division of Pediatric Neurology, Department of Neurology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
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Girisha KM, Pande S, Dalal A, Phadke SR. Untapped opportunities for rare disease gene discovery in India. Am J Med Genet A 2020; 182:3056-3059. [PMID: 32914504 DOI: 10.1002/ajmg.a.61866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/22/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Patil SJ, Karthik GA, Bhavani GS, Bhat V, Matalia J, Shah J, Shukla A, Girisha KM. Bosley-Salih-Alorainy syndrome in patients from India. Am J Med Genet A 2020; 182:2699-2703. [PMID: 32864817 DOI: 10.1002/ajmg.a.61809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 02/05/2020] [Accepted: 07/20/2020] [Indexed: 11/07/2022]
Abstract
Bi-allelic HOXA1 pathogenic variants clinically manifest as two distinct syndromes, Bosley-Salih-Alorainy syndrome (BSAS) and Athabascan brainstem dysgenesis syndrome, mainly reported in two different populations from Saudi Arabia and southwest North America, respectively. Here we report two siblings of Indian origin with BSAS phenotype caused by a novel homozygous exon 2 HOXA1 pathogenic variants.
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Affiliation(s)
- Siddaramappa J Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | | | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Venkatraman Bhat
- Department of Radiology, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Jyoti Matalia
- Department of Pediatric Ophthalmology & Strabismology, Narayana Nethralaya, Bangalore, India
| | - Jhanvi Shah
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
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Pande S, Shukla A, Girisha KM. Trichothiodystrophy type 4 in an Indian family. Am J Med Genet A 2020; 182:2226-2229. [PMID: 33043633 DOI: 10.1002/ajmg.a.61794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 02/20/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
Trichothiodystrophy, non-photosensitive type 4 (TTD4), is a rare genetic disorder with an autosomal recessive mode of inheritance. It is characterized by coarse and brittle hair, anomalies of the tissues derived from the neuro-ectoderm (skin, hair, and nails) and intellectual disability. We herein report two male siblings aged 13 and 16 years with TTD4 and a known homozygous pathogenic variant, c.229del [p.(Arg77Glyfs*76)] in exon 1 of MPLKIP (NM_138701.3). We herein highlight the clinical and molecular findings of the first reported case of TTD4 in probands of Indian ethnicity.
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Affiliation(s)
- Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Kaur P, Kadavigere R, Girisha KM, Shukla A. Recurrent bi-allelic splicing variant c.454+3A>G in TRAPPC4 is associated with progressive encephalopathy and muscle involvement. Brain 2020; 143:e29. [PMID: 32125366 DOI: 10.1093/brain/awaa046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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Narayanan DL, Girisha KM. Genomic Testing for Diagnosis of Genetic Disorders in Children: Chromosomal Microarray and Next—Generation Sequencing. Indian Pediatr 2020. [DOI: 10.1007/s13312-020-1853-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Narayanan DL, Girisha KM. Genomic Testing for Diagnosis of Genetic Disorders in Children: Chromosomal Microarray and Next-Generation Sequencing. Indian Pediatr 2020; 57:549-554. [PMID: 32562398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chromosomal microarray and Next-generation sequencing are two widely used genomic tests that have improved the diagnosis of children with a genetic condition. Chromosomal microarray has become a first-tier test in evaluating children with intellectual disability, multiple malformations and autism due to its higher yield and resolution. Next generation sequencing, that includes targeted panel testing, exome sequencing and whole genome sequencing ends diagnostic odyssey in 25-30% of unselected children with rare monogenic syndromes, especially when the condition is genetically heterogeneous. This article provides a review of these genomic tests for pediatricians.
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Affiliation(s)
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, India. Correspondence to: Dr Girisha KM, Professor, Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576 104, India.
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35
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Dupont MA, Humbert C, Huber C, Siour Q, Guerrera IC, Jung V, Christensen A, Pouliet A, Garfa-Traoré M, Nitschké P, Injeyan M, Millar K, Chitayat D, Shannon P, Girisha KM, Shukla A, Mechler C, Lorentzen E, Benmerah A, Cormier-Daire V, Jeanpierre C, Saunier S, Delous M. Human IFT52 mutations uncover a novel role for the protein in microtubule dynamics and centrosome cohesion. Hum Mol Genet 2020; 28:2720-2737. [PMID: 31042281 DOI: 10.1093/hmg/ddz091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding components of the intraflagellar transport (IFT) complexes have previously been associated with a spectrum of diseases collectively termed ciliopathies. Ciliopathies relate to defects in the formation or function of the cilium, a sensory or motile organelle present on the surface of most cell types. IFT52 is a key component of the IFT-B complex and ensures the interaction of the two subcomplexes, IFT-B1 and IFT-B2. Here, we report novel IFT52 biallelic mutations in cases with a short-rib thoracic dysplasia (SRTD) or a congenital anomaly of kidney and urinary tract (CAKUT). Combining in vitro and in vivo studies in zebrafish, we showed that SRTD-associated missense mutation impairs IFT-B complex assembly and IFT-B2 ciliary localization, resulting in decreased cilia length. In comparison, CAKUT-associated missense mutation has a mild pathogenicity, thus explaining the lack of skeletal defects in CAKUT case. In parallel, we demonstrated that the previously reported homozygous nonsense IFT52 mutation associated with Sensenbrenner syndrome [Girisha et al. (2016) A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin. Genet., 90, 536-539] leads to exon skipping and results in a partially functional protein. Finally, our work uncovered a novel role for IFT52 in microtubule network regulation. We showed that IFT52 interacts and partially co-localized with centrin at the distal end of centrioles where it is involved in its recruitment and/or maintenance. Alteration of this function likely contributes to centriole splitting observed in Ift52-/- cells. Altogether, our findings allow a better comprehensive genotype-phenotype correlation among IFT52-related cases and revealed a novel, extra-ciliary role for IFT52, i.e. disruption may contribute to pathophysiological mechanisms.
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Affiliation(s)
- Marie Alice Dupont
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Camille Humbert
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Céline Huber
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Quentin Siour
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Ida Chiara Guerrera
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Vincent Jung
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Anni Christensen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Aurore Pouliet
- Genomics Core Facility, Imagine Institute and Structure Fédérative de Recherche Necker, INSERM UMR1163 and INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Meriem Garfa-Traoré
- Cell Imaging Platform UMS 24, Structure Fédérative de Recherche Necker, Inserm US24/CNRS UMS3633, Paris, France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Bioinformatics Core Facility, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Marie Injeyan
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Kathryn Millar
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Charlotte Mechler
- Assistance Publique - Hôpitaux de Paris, Louis Mourier Hospital, Colombes, France
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marion Delous
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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Kaur P, Sharma S, Kadavigere R, Girisha KM, Shukla A. Novel variant p.(Ala102Thr) in
SDHB
causes mitochondrial complex II deficiency: Case report and review of the literature. Ann Hum Genet 2020; 84:345-351. [DOI: 10.1111/ahg.12377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics Kasturba Medical College, Manipal Manipal Academy of Higher Education Manipal India
| | - Suvasini Sharma
- Neurology Division Department of Pediatrics Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital New Delhi India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis & Imaging Kasturba Medical College, Manipal Manipal Academy of Higher Education Manipal India
| | - Katta Mohan Girisha
- Department of Medical Genetics Kasturba Medical College, Manipal Manipal Academy of Higher Education Manipal India
| | - Anju Shukla
- Department of Medical Genetics Kasturba Medical College, Manipal Manipal Academy of Higher Education Manipal India
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37
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Lewis SS, Girisha KM. Whole exome sequencing identifies a novel pathogenic variation [p.(Gly194valfs*7)] in SLC45A2 in the homozygous state in multiple members of a family with oculocutaneous albinism in southern India. Clin Exp Dermatol 2019; 45:409-413. [PMID: 31630438 DOI: 10.1111/ced.14126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 01/16/2023]
Abstract
Deleterious mutations within the SLC45A2 gene, encoding membrane-associated transporter protein (MATP), are responsible for type 4 oculocutaneous albinism. The cytogenetic location of SLC45A2 is 5p13.2 and it comprises seven exons located over around 40 kb. Its encoded protein, MATP, is 530 amino acids long and has 12 putative transmembrane domains. MATP is synthesized within melanocytes. It is in these cells that melanogenesis takes place and the melanin is contained within specialized organelles called melanosomes. Previous studies have shown that when MATP expression was reduced using small interfering RNA in MNT-1 melanoma cells, pH was lowered within melanosomes, they became poorly melanized and tyrosinase activity within melanocytes was also reduced. This type of albinism produces a broad spectrum of phenotypes, ranging from complete absence of melanin to brown hair and brown irides. In the current study, blood was collected from a family in which four members had oculocutaneous albinism, showing a complete absence of melanin in skin, hair and eyes. Screening of the TYR gene using the extracted DNA showed no mutation and therefore whole exome sequencing analysis was performed. A novel deletion mutation c.579delG [p.(Gly194Valfs*7)] in the SLC45A2 gene, predicted to be pathogenic and to result in both frameshift and premature termination of the MATP chain, was identified. These data add to the information pertaining to the mutation spectrum of OCA4.
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Affiliation(s)
- S S Lewis
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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38
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Uttarilli A, Shah H, Shukla A, Girisha KM. A review of skeletal dysplasia research in India. J Postgrad Med 2019; 64:98-103. [PMID: 29692401 PMCID: PMC5954821 DOI: 10.4103/jpgm.jpgm_527_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We aimed to review the contributions by Indian researchers to the subspecialty of skeletal dysplasias (SDs). Literature search using specific keywords in PubMed was performed to retrieve all the published literature on SDs as on July 6, 2017. All published literature on SDs wherein at least one author was from an Indian institute was included. Publications were grouped into different categories based on the major emphasis of the research paper. Five hundred and forty publications in English language were retrieved and categorized into five different groups. The publications were categorized as reports based on: (i) phenotypes (n = 437), (ii) mutations (n = 51), (iii) novel genes (n = 9), (iv) therapeutic interventions (n = 31), and (v) reviews (n = 12). Most of the publications were single-patient case reports describing the clinical and radiological features of the patients affected with SDs (n = 352). We enlisted all the significant Indian contributions. We have also highlighted the reports in which Indians have contributed to discovery of new genes and phenotypes. This review highlights the substantial Indian contributions to SD research, which is poised to reach even greater heights given the size and structure of our population, technological advances, and expanding national and international collaborations.
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Affiliation(s)
- A Uttarilli
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - H Shah
- Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - A Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
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39
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Sekiguchi F, Tsurusaki Y, Okamoto N, Teik KW, Mizuno S, Suzumura H, Isidor B, Ong WP, Haniffa M, White SM, Matsuo M, Saito K, Phadke S, Kosho T, Yap P, Goyal M, Clarke LA, Sachdev R, McGillivray G, Leventer RJ, Patel C, Yamagata T, Osaka H, Hisaeda Y, Ohashi H, Shimizu K, Nagasaki K, Hamada J, Dateki S, Sato T, Chinen Y, Awaya T, Kato T, Iwanaga K, Kawai M, Matsuoka T, Shimoji Y, Tan TY, Kapoor S, Gregersen N, Rossi M, Marie-Laure M, McGregor L, Oishi K, Mehta L, Gillies G, Lockhart PJ, Pope K, Shukla A, Girisha KM, Abdel-Salam GMH, Mowat D, Coman D, Kim OH, Cordier MP, Gibson K, Milunsky J, Liebelt J, Cox H, El Chehadeh S, Toutain A, Saida K, Aoi H, Minase G, Tsuchida N, Iwama K, Uchiyama Y, Suzuki T, Hamanaka K, Azuma Y, Fujita A, Imagawa E, Koshimizu E, Takata A, Mitsuhashi S, Miyatake S, Mizuguchi T, Miyake N, Matsumoto N. Genetic abnormalities in a large cohort of Coffin-Siris syndrome patients. J Hum Genet 2019; 64:1173-1186. [PMID: 31530938 DOI: 10.1038/s10038-019-0667-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/13/2019] [Accepted: 08/25/2019] [Indexed: 01/15/2023]
Abstract
Coffin-Siris syndrome (CSS, MIM#135900) is a congenital disorder characterized by coarse facial features, intellectual disability, and hypoplasia of the fifth digit and nails. Pathogenic variants for CSS have been found in genes encoding proteins in the BAF (BRG1-associated factor) chromatin-remodeling complex. To date, more than 150 CSS patients with pathogenic variants in nine BAF-related genes have been reported. We previously reported 71 patients of whom 39 had pathogenic variants. Since then, we have recruited an additional 182 CSS-suspected patients. We performed comprehensive genetic analysis on these 182 patients and on the previously unresolved 32 patients, targeting pathogenic single nucleotide variants, short insertions/deletions and copy number variations (CNVs). We confirmed 78 pathogenic variations in 78 patients. Pathogenic variations in ARID1B, SMARCB1, SMARCA4, ARID1A, SOX11, SMARCE1, and PHF6 were identified in 48, 8, 7, 6, 4, 1, and 1 patients, respectively. In addition, we found three CNVs including SMARCA2. Of particular note, we found a partial deletion of SMARCB1 in one CSS patient and we thoroughly investigated the resulting abnormal transcripts.
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Affiliation(s)
- Futoshi Sekiguchi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Kanagawa, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Keng Wee Teik
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Seiji Mizuno
- Department of Clinical Genetics, Central Hospital, Aichi Developmental Disability Center, Kasugai, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | | | - Winnie Peitee Ong
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Muzhirah Haniffa
- Department of Genetics, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Mari Matsuo
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Shubha Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Patrick Yap
- Genetic Health Service New Zealand, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Manisha Goyal
- Rare Disease Clinic, J K Lone Hospital, SMS Medical College, Jaipur, Rajasthan, India
| | - Lorne A Clarke
- British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Richard J Leventer
- Royal Children's Hospital Department of Neurology, Murdoch Children's Research Institute and University of Melbourne Department of Pediatrics, Parkville, 3052, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | | | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Yoshiya Hisaeda
- Department of Neonatology, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Kenji Shimizu
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | - Keisuke Nagasaki
- Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Junpei Hamada
- Department of Pediatrics, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takashi Sato
- Asahikawa-Kosei General Hospital, Hokkaido, Japan
| | - Yasutsugu Chinen
- Department of Child Health and Welfare, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeo Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kougoro Iwanaga
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Kawai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Matsuoka
- Department of General Pediatrics, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Okinawa, Japan
| | - Yoshikazu Shimoji
- Department of General Pediatrics, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Okinawa, Japan
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Seema Kapoor
- Division of Genetics, Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
| | | | - Massimiliano Rossi
- Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, and INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, UCBL1, Bron, France
| | - Mathieu Marie-Laure
- Hospices Civils de Lyon, Service de Génétique, Centre de Référence Anomalies du Développement, and INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, UCBL1, Bron, France
| | - Lesley McGregor
- South Australian Clinical Genetics Service, SA Pathology, Women's and Children's Hospital, Adelaide, Australia
| | - Kimihiko Oishi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Victoria, Australia
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Victoria, Australia
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - David Mowat
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - David Coman
- Department of Paediatrics, The Wesley Hospital, Brisbane, QLD, Australia
| | - Ok Hwa Kim
- Department of Radiology, Ajou University Hospital, Suwon, Korea
| | | | - Kate Gibson
- Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | | | - Jan Liebelt
- South Australian Clinical Genetics Services, Women's and Children's Hospital, North Adelaide, Australia
| | - Helen Cox
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham Women's Hospital, Edgbaston, Birmingham, B15 2TG, UK
| | - Salima El Chehadeh
- Service de Genetique Medicale, Hopital de Hautepierre, Strasbourg, France
| | | | - Ken Saida
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Gaku Minase
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Toshifumi Suzuki
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Eri Imagawa
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate school of medicine, Yokohama City University, Yokohama, Japan.
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40
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Pehlivan D, Bayram Y, Gunes N, Coban Akdemir Z, Shukla A, Bierhals T, Tabakci B, Sahin Y, Gezdirici A, Fatih JM, Gulec EY, Yesil G, Punetha J, Ocak Z, Grochowski CM, Karaca E, Albayrak HM, Radhakrishnan P, Erdem HB, Sahin I, Yildirim T, Bayhan IA, Bursali A, Elmas M, Yuksel Z, Ozdemir O, Silan F, Yildiz O, Yesilbas O, Isikay S, Balta B, Gu S, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Boerwinkle E, Gibbs RA, Tsiakas K, Hempel M, Girisha KM, Gul D, Posey JE, Elcioglu NH, Tuysuz B, Lupski JR. The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance. Am J Hum Genet 2019; 105:132-150. [PMID: 31230720 PMCID: PMC6612529 DOI: 10.1016/j.ajhg.2019.05.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 01/29/2023] Open
Abstract
Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.
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Affiliation(s)
- Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Burcu Tabakci
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey
| | - Yavuz Sahin
- Department of Medical Genetics, Necip Fazıl City Hospital, Kahramanmaras 46050, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul 34093, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Ocak
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hatice Mutlu Albayrak
- Department of Pediatrics, Division of Pediatric Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55270, Turkey
| | - Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Ibrahim Sahin
- Department of Medical Genetics, University of Erzurum, School of Medicine, Erzurum 25240, Turkey
| | - Timur Yildirim
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Ilhan A Bayhan
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Aysegul Bursali
- Department of Orthopedics and Traumatology, Baltalimani Bone Diseases Training and Research Hospital, Istanbul 34470, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Zafer Yuksel
- Medical Genetics Clinic, Mersin Women and Children Hospital, Mersin 33330, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Onur Yildiz
- Department of Medical Genetics, Faculty of Medicine, Onsekiz Mart University, Canakkale 17000, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, University of Health Sciences, Van Training and Research Hospital, Van 65130, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep 27000, Turkey
| | - Burhan Balta
- Department of Medical Genetics, Kayseri Training and Research Hospital, Kayseri 38080, Turkey
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Konstantinos Tsiakas
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul 34854, Turkey; Eastern Mediterranean University School of Medicine, Cyprus, Mersin 10, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa Medical Faculty, Istanbul 34096, Turkey
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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41
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Kaur P, Wamelink MMC, van der Knaap MS, Girisha KM, Shukla A. Confirmation of a Rare Genetic Leukoencephalopathy due to a Novel Bi-allelic Variant in RPIA. Eur J Med Genet 2019; 62:103708. [PMID: 31247379 DOI: 10.1016/j.ejmg.2019.103708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/02/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Ribose 5-phosphate isomerase deficiency is a rare genetic leukoencephalopathy caused by pathogenic sequence variants in RPIA, that encodes ribose 5-phosphate isomerase, an enzyme in the pentose phosphate pathway. Till date, only three individuals with ribose 5-phosphate isomerase deficiency have been described in literature. We report on a subject with RPIA associated progressive leukoencephalopathy with elevated urine arabitol and ribitol levels and a novel missense variant c.770T > C p.(Ile257Thr) in exon 8 of RPIA. We also compare the phenotypes of all the four subjects. Our report confirms the phenotype and the genetic cause of this condition.
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Affiliation(s)
- Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Mirjam M C Wamelink
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Clinical Chemistry, Metabolic Laboratory, Amsterdam Neuroscience, De Boelelaan, 1117, Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- Pediatric Neurology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam Neuroscience, The Netherlands; Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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42
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Moirangthem A, Narayanan DL, Jacob P, Nishimura G, Mortier G, Girisha KM. Report of second case and clinical and molecular characterization of Eiken syndrome. Clin Genet 2018; 94:457-460. [PMID: 29987841 DOI: 10.1111/cge.13413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/29/2022]
Abstract
We report a boy with Eiken syndrome caused by a homozygous missense variant in Parathyroid hormone 1 receptor (PTH1R) c.103G > A [p.(Glu35Lys)]. Eiken syndrome is a very rare skeletal dysplasia due to bi-allelic variants in PTH1R. Only one affected family has been known to-date. The hallmarks include delayed ossification of bone including the epiphyses, pubic symphysis, and primary ossification centers of the short tubular bones, coarse bone trabeculae, and modeling abnormalities. The phenotype being described here recapitulates the delayed ossification and modeling abnormalities of Eiken syndrome. In addition, supernumerary epiphyses of the tubular bones of the hands and primary failure of eruption of teeth were observed in our proband. This report characterizes Eiken syndrome and confirms that bi-allelic hypomorphic variants in PTH1R are probably to cause this condition.
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Affiliation(s)
- A Moirangthem
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - D L Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - P Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - G Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - G Mortier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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43
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Szenker-Ravi E, Altunoglu U, Leushacke M, Bosso-Lefèvre C, Khatoo M, Thi Tran H, Naert T, Noelanders R, Hajamohideen A, Beneteau C, de Sousa SB, Karaman B, Latypova X, Başaran S, Yücel EB, Tan TT, Vlaminck L, Nayak SS, Shukla A, Girisha KM, Le Caignec C, Soshnikova N, Uyguner ZO, Vleminckx K, Barker N, Kayserili H, Reversade B. RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6. Nature 2018; 557:564-569. [PMID: 29769720 DOI: 10.1038/s41586-018-0118-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
The four R-spondin secreted ligands (RSPO1-RSPO4) act via their cognate LGR4, LGR5 and LGR6 receptors to amplify WNT signalling1-3. Here we report an allelic series of recessive RSPO2 mutations in humans that cause tetra-amelia syndrome, which is characterized by lung aplasia and a total absence of the four limbs. Functional studies revealed impaired binding to the LGR4/5/6 receptors and the RNF43 and ZNRF3 transmembrane ligases, and reduced WNT potentiation, which correlated with allele severity. Unexpectedly, however, the triple and ubiquitous knockout of Lgr4, Lgr5 and Lgr6 in mice did not recapitulate the known Rspo2 or Rspo3 loss-of-function phenotypes. Moreover, endogenous depletion or addition of exogenous RSPO2 or RSPO3 in triple-knockout Lgr4/5/6 cells could still affect WNT responsiveness. Instead, we found that the concurrent deletion of rnf43 and znrf3 in Xenopus embryos was sufficient to trigger the outgrowth of supernumerary limbs. Our results establish that RSPO2, without the LGR4/5/6 receptors, serves as a direct antagonistic ligand to RNF43 and ZNRF3, which together constitute a master switch that governs limb specification. These findings have direct implications for regenerative medicine and WNT-associated cancers.
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Affiliation(s)
| | - Umut Altunoglu
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Marc Leushacke
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Célia Bosso-Lefèvre
- Institute of Medical Biology, A*STAR, Singapore, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | - Muznah Khatoo
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Hong Thi Tran
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rivka Noelanders
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | | | - Sergio B de Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,University Clinic of Genetics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Birsen Karaman
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Xenia Latypova
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Seher Başaran
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Esra Börklü Yücel
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey
| | - Thong Teck Tan
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - Lena Vlaminck
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,INSERM, UMR1238, Bone Sarcoma and Remodeling of Calcified Tissue, Université Bretagne Loire, Nantes, France
| | | | - Zehra Oya Uyguner
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Center for Medical Genetics, Ghent University, Ghent, Belgium.
| | - Nick Barker
- Institute of Medical Biology, A*STAR, Singapore, Singapore. .,Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan. .,Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK.
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey. .,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.
| | - Bruno Reversade
- Institute of Medical Biology, A*STAR, Singapore, Singapore. .,Department of Paediatrics, National University of Singapore, Singapore, Singapore. .,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey. .,Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore. .,Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands.
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Mrosk J, Bhavani GS, Shah H, Hecht J, Krüger U, Shukla A, Kornak U, Girisha KM. Diagnostic strategies and genotype-phenotype correlation in a large Indian cohort of osteogenesis imperfecta. Bone 2018; 110:368-377. [PMID: 29499418 DOI: 10.1016/j.bone.2018.02.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
Osteogenesis Imperfecta (OI) is a clinically and genetically heterogeneous disorder. Although differential diagnosis is greatly facilitated by next generation sequencing, its availability can vary considerably. In this study, we compared targeted gene panel or exome sequencing with clinical scoring and grouping in a cohort of 50 OI index patients recruited by a single Indian clinical center in an unselected fashion. In 48 patients we observed a total of 24 novel mutations and 24 known OI mutations, of which several were recurrent. In one patient neither gene panel nor exome sequencing revealed any significant mutation and another patient harbored a class III COL1A1 intronic variant. The percentage of autosomal recessive forms due to mutations in BMP1, FKBP10, LEPRE1, SERPINF1, and WNT1 was unusually high (48%). Grouping according to phenotypic and radiographic features revealed four individuals with Bruck syndrome due to FKBP10 mutations, three patients with hypertrophic callus caused by IFITM5 mutations, and twenty with pronounced bone bowing, of which eight carried WNT1 mutations. There was a clear correlation between genotype and phenotype severity: IFITM5=LEPRE1>WNT1>SERPINF1>COL1A1 (qualitative)>BMP1>FKBP10>COL1A2 (qualitative)>COL1A1 (quantitative)>COL1A2 (quantitative). In one patient we found heterozygous variants in COL1A1 and COL1A2 inherited from parents without an obvious bone phenotype indicating that both variants might contribute to the phenotype. Our findings demonstrate the clinical utility of gene panel testing for OI, but in cases with contractures, hypertrophic callus formation, or - to some extent - extensive bowing single gene analysis might still be more cost-effective.
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Affiliation(s)
- Julia Mrosk
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Pediatric Orthopedics Services, Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Jochen Hecht
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ulrike Krüger
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Max Planck Institute for Molecular Genetics, FG Development & Disease, Berlin, Germany.
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
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45
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Salian S, Shukla A, Shah H, Bhat SN, Bhat VR, Nampoothiri S, Shenoy R, Phadke SR, Hariharan SV, Girisha KM. Seven additional families with spondylocarpotarsal synostosis syndrome with novel biallelic deleterious variants in FLNB. Clin Genet 2018; 94:159-164. [PMID: 29566257 DOI: 10.1111/cge.13252] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/15/2018] [Accepted: 03/17/2018] [Indexed: 02/01/2023]
Abstract
The location and/or type of variants in FLNB result in a spectrum of osteochondrodysplasias ranging from mild forms, like spondylocarpotarsal synostosis syndrome and Larsen syndrome, to severe perinatal lethal forms, such as atelosteogenesis I and III and Boomerang dysplasia. Spondylocarpotarsal synostosis syndrome is characterized by disproportionate short stature, vertebral anomalies and fusion of carpal and tarsal bones. Biallelic loss-of-function variants in FLNB are known to cause spondylocarpotarsal synostosis syndrome and 9 families and 9 pathogenic variants have been reported so far. We report clinical features of 10 additional patients from 7 families with spondylocarpotarsal synostosis syndrome due to 7 novel deleterious variants in FLNB, thus expanding the clinical and molecular repertoire of spondylocarpotarsal synostosis syndrome. Our report validates key clinical (fused thoracic vertebrae and carpal and tarsal coalition) and molecular (truncating variants in FLNB) characteristics of this condition.
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Affiliation(s)
- S Salian
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - A Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - H Shah
- Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S N Bhat
- Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - V R Bhat
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - R Shenoy
- Department of Pediatrics, KS Hegde Medical Academy, Mangalore, Karnataka, India
| | - S R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - S V Hariharan
- Department of Pediatrics, Sree Avittom Thirunal Hospital, Government Medical College, Trivandrum, Kerala, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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46
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Nakatsuka N, Moorjani P, Rai N, Sarkar B, Tandon A, Patterson N, Bhavani GS, Girisha KM, Mustak MS, Srinivasan S, Kaushik A, Vahab SA, Jagadeesh SM, Satyamoorthy K, Singh L, Reich D, Thangaraj K. The promise of discovering population-specific disease-associated genes in South Asia. Nat Genet 2017; 49:1403-1407. [PMID: 28714977 PMCID: PMC5675555 DOI: 10.1038/ng.3917] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/21/2017] [Indexed: 12/21/2022]
Abstract
The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identified 81 unique groups, 14 of which had estimated census sizes of more than 1 million, that descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. We identified multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an underappreciated opportunity for decreasing disease burden among South Asians through discovery of and testing for recessive disease-associated genes.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Arti Tandon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, India
| | | | - Amit Kaushik
- Amity Institute of Biotechnology, Amity University, Noida, India
| | | | | | | | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
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47
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Kotabagi S, Shah H, Shukla A, Girisha KM. Second family provides further evidence for causation of Steel syndrome by biallelic mutations in COL27A1. Clin Genet 2017; 92:323-326. [PMID: 28276056 DOI: 10.1111/cge.13006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/20/2017] [Accepted: 03/01/2017] [Indexed: 11/27/2022]
Abstract
Steel syndrome is a rare disorder of the skeleton characterized by facial dysmorphism, short stature, carpal coalition, dislocated radial heads, bilateral hip dislocation and vertical talus. Homozygous variants in COL27A1 were reported in an extending family from Puerto Rico. Here, we report a 5-year-old girl from a non-consanguineous family with facial dysmorphism, short stature, carpal coalition, dislocation of radial heads, bilateral hip dislocation, scoliosis and vertical talus. Exome sequencing identified 2 novel compound heterozygous variants c.521_528del (p.(Cys174Serfs*34)) and c.2119C>T (p.(Arg707*)) in COL27A1 in this child and the parents were heterozygous carriers. We hence report the second molecularly proven case of Steel syndrome and the first case to be reported among non-Puerto Rican population. Our report further validates the role of COL27A1 mutations in causation of Steel syndrome.
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Affiliation(s)
- S Kotabagi
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - H Shah
- Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, India
| | - A Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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48
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Shukla A, Upadhyai P, Shah J, Neethukrishna K, Bielas S, Girisha KM. Autosomal recessive spinocerebellar ataxia 20: Report of a new patient and review of literature. Eur J Med Genet 2016; 60:118-123. [PMID: 27913285 DOI: 10.1016/j.ejmg.2016.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/10/2016] [Accepted: 11/20/2016] [Indexed: 10/20/2022]
Abstract
Inherited ataxias are an extremely heterogeneous group of disorders. Autosomal recessive spinocerebellar ataxia 20 (SCAR20) is a recently described disorder characterized by intellectual disability, ataxia, coarse facial features, progressive loss of Purkinje cells in the cerebellum and often hearing loss and skeletal abnormalities. Mutations in the gene SNX14, which plays an important role in autophagy, have been found to cause SCAR20. The unique clinical findings of progressive coarsening of facial features makes the clinical phenotype recognizable among the various hereditary ataxias. Here we report on a child with a novel missense mutation in the SNX14 gene that appears to be debilitating for protein conformation, function and review the previously reported cases from 15 families.
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Affiliation(s)
- Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Jhanvi Shah
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - K Neethukrishna
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India.
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49
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Girisha KM, Kortüm F, Shah H, Alawi M, Dalal A, Bhavani GS, Kutsche K. A novel multiple joint dislocation syndrome associated with a homozygous nonsense variant in the EXOC6B gene. Eur J Hum Genet 2016; 24:1206-10. [PMID: 26669664 PMCID: PMC4970677 DOI: 10.1038/ejhg.2015.261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/04/2015] [Accepted: 11/15/2015] [Indexed: 01/12/2023] Open
Abstract
We report two brothers from a consanguineous couple with spondyloepimetaphyseal dysplasia (SEMD), multiple joint dislocations at birth, severe joint laxity, scoliosis, gracile metacarpals and metatarsals, delayed bone age and poorly ossified carpal and tarsal bones, probably representing a yet uncharacterized SEMD with laxity and dislocations. This condition has clinical overlap with autosomal dominantly inherited SEMD with joint laxity, leptodactylic type caused by recurrent missense variants in the kinesin family member 22 gene (KIF22). Single-nucleotide polymorphism array analysis and whole-exome sequencing in the two affected siblings revealed a shared homozygous nonsense variant [c.906T>A/p.(Tyr302*)] in EXOC6B as the most likely cause. EXOC6B encodes a component of the exocyst complex required for tethering secretory vesicles to the plasma membrane. As transport of vesicles from the golgi apparatus to the plasma membrane occurs through kinesin motor proteins along microtubule tracks, the function of EXOC6B is linked to KIF22 suggesting a common pathogenic mechanism in skeletal dysplasias with joint laxity and dislocations.
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Affiliation(s)
- Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hitesh Shah
- Division of Pediatric Orthopedics, Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, India
| | - Malik Alawi
- University Medical Center Hamburg-Eppendorf, Bioinformatics Service Facility, Hamburg, Germany
- Center for Bioinformatics, University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz-Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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50
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Hebbar M, Prasada L H, Bhowmik AD, Trujillano D, Shukla A, Chakraborti S, Kandaswamy KK, Rolfs A, Kamath N, Dalal A, Bielas S, Girisha KM. Homozygous deletion of exons 2 and 3 of NPC2 associated with Niemann-Pick disease type C. Am J Med Genet A 2016; 170:2486-9. [PMID: 27271431 DOI: 10.1002/ajmg.a.37794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/30/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Harsha Prasada L
- Department of Pediatrics, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Andhra Pradesh, India
| | | | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Shrijeet Chakraborti
- Department of Pathology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | | | - Arndt Rolfs
- Centogene AG, Rostock, Mecklenburg-Vorpommern, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Mecklenburg-Vorpommern, Germany
| | - Nutan Kamath
- Department of Pediatrics, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Andhra Pradesh, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
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