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Cho JH, Hwang S, Kwak YH, Yum M, Seo GH, Koh J, Ju YS, Yoon J, Kang M, Do H, Kim S, Kim G, Bae H, Lee BH. Clinical and genetic characteristics of three patients with congenital insensitivity to pain with anhidrosis: Case reports and a review of the literature. Mol Genet Genomic Med 2024; 12:e2430. [PMID: 38581121 PMCID: PMC10997844 DOI: 10.1002/mgg3.2430] [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: 01/24/2024] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder caused by loss-of-function mutations of the NTRK1 gene, affecting the autonomic and sensory nervous system. Clinical manifestation is varied and includes recurrent fever, pain insensitivity, anhidrosis, self-mutilating behavior, and intellectual disability. METHODS Clinical and genetic features were assessed in two males and one female with genetically confirmed CIPA using exome or genome sequencing. RESULTS CIPA symptoms including recurrent fever, pain insensitivity, and anhidrosis manifested at the age of 1 year (age range: 0.3-8 years). Two patients exhibited self-mutilation tendencies, intellectual disability, and developmental delay. Four NTRK1 (NM_002529.3) mutations, c.851-33T>A (p.?), c.2020G>T (p.Asp674Tyr), c.2303C>T (p.Pro768Leu), and c.574-156_850+1113del (exons 5-7 del) were identified. Two patients exhibited early onset and severe phenotype, being homozygous for c.851-33T>A (p.?) mutations and compound heterozygous for c.851-33T>A (p.?) and c.2020G>T (p.Asp674Tyr) mutation of NTRK1. The third patient with compound heterozygous mutations of c.2303C>T (p.Pro768Leu) and c.574-156_850+1113del (exons 5-7 del) displayed a late onset and milder clinical manifestation. CONCLUSION All three patients exhibited variable phenotypes and disease severity. This research enriches our understanding of clinical and genetic aspects of CIPA, highlighting variable phenotypes and disease severity.
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Affiliation(s)
- Jun Hee Cho
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Soojin Hwang
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yoon Hae Kwak
- Department of Orthopedic Surgery, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Mi‐Sun Yum
- Department of Pediatric NeurologyAsan Medical Center, University of Ulsan College of MedicineSeoulRepublic of Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3billion, Inc.SeoulRepublic of Korea
| | | | | | - Ji‐Hee Yoon
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Minji Kang
- Asan Medical CenterAsan Institute for Life SciencesSeoulRepublic of Korea
| | - Hyo‐Sang Do
- Asan Medical CenterAsan Institute for Life SciencesSeoulRepublic of Korea
| | - Soyoung Kim
- Asan Medical CenterAsan Institute for Life SciencesSeoulRepublic of Korea
| | - Gu‐Hwan Kim
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Hyunwoo Bae
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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Song Y, Elwafa RAHA, Omar OM, Seo GH, Lee H. A case report of an Egyptian family with familial hypercholesterolemia and an exonic LINE-1 insertion in LDLR. Mol Genet Genomic Med 2024; 12:e2410. [PMID: 38433605 PMCID: PMC10910215 DOI: 10.1002/mgg3.2410] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/06/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Familial hypercholesterolemia (MIM: PS143890) is a genetic disorder characterized by an increase in blood cholesterol. LDLR is one of the genes which their defect contributes to the disorder. Affected individuals may carry a heterozygous variant or homozygous/compound heterozygous variants and those with biallelic pathogenic variants present more severe symptoms. METHOD We report an Egyptian family with familial hypercholesterolemia. Both the proband and parents have the disorder while a sibling is unaffected. Exome sequencing was performed to identify the causal variant. RESULTS LINE-1 insertion in exon 7 of LDLR was identified. Both parents have a heterozygous variant while the proband has a homozygous variant. The unaffected sibling did not carry the variant. DISCUSSION This insertion may contribute to the high prevalence of hypercholesterolemia in Egypt and the finding underscores the importance of implementing mobile element insertion caller in routine bioinformatics pipeline.
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Affiliation(s)
| | | | - Omneya Magdy Omar
- Department of Pediatrics, Faculty of MedicineAlexandria UniversityAlexandriaEgypt
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Redfield SE, De-la-Torre P, Zamani M, Wang H, Khan H, Morris T, Shariati G, Karimi M, Kenna MA, Seo GH, Xu H, Lu W, Naz S, Galehdari H, Indzhykulian AA, Shearer AE, Vona B. PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss. Hum Genet 2024; 143:311-329. [PMID: 38459354 PMCID: PMC11043200 DOI: 10.1007/s00439-024-02649-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/21/2024] [Indexed: 03/10/2024]
Abstract
Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modeling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modeling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.
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Affiliation(s)
- Shelby E Redfield
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA
| | - Pedro De-la-Torre
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Hanjun Wang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Hina Khan
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Tyler Morris
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Karimi
- Khuzestan Cochlear Implantation Center (Tabassom), Ahvaz, Iran
| | - Margaret A Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
| | | | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Wei Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jian-She Road, Zhengzhou, 450052, China
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Artur A Indzhykulian
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA.
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - A Eliot Shearer
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA.
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073, Göttingen, Germany.
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany.
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Ryu SW, Yoon J, Kim D, Han B, Han H, Han J, Lee H, Seo GH, Lee BH. Identification of a complex intrachromosomal inverted insertion in the long arm of chromosome 9 as a cause of tuberous sclerosis complex in a Korean family. Mol Genet Genomic Med 2024; 12:e2330. [PMID: 38265426 PMCID: PMC10958175 DOI: 10.1002/mgg3.2330] [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: 07/09/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder, caused by a loss-of-function of either TSC1 or TSC2 gene. However, in 10%-15% TSC patients there is no pathogenic variant identified in either TSC1 or TSC2 genes based on standard clinical testing. METHODS In this study, genome sequencing was performed for families with clinical diagnosis of TSC with negative results from TSC1 and TSC2 single-gene tests. RESULTS Herein, we report a family presenting a classical TSC phenotype with an unusual, complex structural variant involving the TSC1 gene: an intrachromosomal inverted insertion in the long arm of chromosome 9. We speculate that the inverted 9q33.3q34.13 region was inserted into the q31.2 region with the 3'-end of the breakpoint of the inversion being located within the TSC1 gene, resulting in premature termination of TSC1. CONCLUSIONS In this study, we demonstrate the utility of genome sequencing for the identification of complex chromosomal rearrangement. Because the breakpoints are located within the deep intronic/intergenic region, this copy-neutral variant was missed by the TSC1 and TSC2 single-gene tests and contributed to an unknown etiology. Together, this finding suggests that complex structural variants may be underestimated causes for the etiology of TSC.
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Affiliation(s)
| | - Ji‐Hee Yoon
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | | | | | | | | | | | | | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's HospitalUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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Ooi JCE, Azman A, Chan MY, Toh ESY, Seo GH, Kim JH, Yakob Y, Chia YK. Progressive ataxia, ophthalmoparesis, and hypogonadotropic hypogonadism in a family with a novel variant in the KIFBP gene. Clin Genet 2024; 105:228-230. [PMID: 37903629 DOI: 10.1111/cge.14448] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023]
Abstract
A novel homozygous variant in KIFBP was identified in a consanguineous family with four sibs affected by Goldberg-Sphrintzen Syndrome (GOSHS). We report for the first time, early-adulthood-onset progressive ataxia, opthalmoparesis, and hypogonadotropic hypogonadism in GOSHS.
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Affiliation(s)
| | - Amelia Azman
- Molecular Diagnostics Unit, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Mei-Yan Chan
- Genetics Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | | | | | | | - Yusnita Yakob
- Molecular Diagnostics Unit, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Yuen Kang Chia
- Neurology Unit, Queen Elizabeth Hospital, Kota Kinabalu, Malaysia
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Ko YJ, Rhie S, Baek J, Seo GH, Lee SY. Familial focal segmental glomerulosclerosis associated with a WT1 gene missense mutation: A case report. J PAK MED ASSOC 2024; 74:149-152. [PMID: 38219185 DOI: 10.47391/jpma.8251] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Focal s egmental glomerulosclerosis (F SGS) can cause protei nuria and loss o f k idney fun ction, leading to e ndstage renal di s ease (ESRD). Podocyte injury is the ce ntral pathophysiologi cal mechanis m of hereditary FSGS. Numerous mutations in genes e ncoding or affe cting the transcriptional regulation of podocyte cell compar tments have been detected in patients with genetic FSGS. Herein, we report a rare case of familial FSGS with an autosomal dominant WT1 mutation. A 63-year- old man developed pro teinuri a; his reading showed over 1g prote in/day. A pa thological diagn osis of FSG S was made after rena l biops y. H is elder brother an d a 36-year- old son also had ESRD. Heterozygous variant of WT1 (NM_024426.4) c.1373G>A (p.Arg458Gln ) mi s sense was dete cted in the patient a nd his son , by whole-exome sequen cing. Although genetic screening is not a par t of routine practice, it s hould be per for med in such cases to a id a ppropriate tre atment options sel ecting, revealing extra ren al symptoms, and family planning.
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Affiliation(s)
- Yun Jung Ko
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Seonkyeong Rhie
- Department of Paediatrics, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Jihyun Baek
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | | | - So-Young Lee
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
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Redfield SE, De-la-Torre P, Zamani M, Wang H, Khan H, Morris T, Shariati G, Karimi M, Kenna MA, Seo GH, Xu H, Lu W, Naz S, Galehdari H, Indzhykulian AA, Shearer AE, Vona B. PKHD1L1, A Gene Involved in the Stereocilia Coat, Causes Autosomal Recessive Nonsyndromic Hearing Loss. medRxiv 2023:2023.10.08.23296081. [PMID: 37873491 PMCID: PMC10593026 DOI: 10.1101/2023.10.08.23296081] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modelling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modelling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.
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Affiliation(s)
- Shelby E. Redfield
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
| | - Pedro De-la-Torre
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Hanjun Wang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Hina Khan
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Tyler Morris
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Karimi
- Khuzestan Cochlear Implantation Center (Tabassom), Ahvaz, Iran
| | - Margaret A. Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
| | | | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Wei Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jian-she Road, Zhengzhou, 450052, China
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Artur A. Indzhykulian
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - A. Eliot Shearer
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
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Seo Y, Kim TY, Won D, Choi JR, Seo GH, Lee ST, Han J. PTPN23 Neurodevelopmental Disorder Presenting With Optic Atrophy and Spasmus Nutans-Like Nystagmus. J Neuroophthalmol 2023; 43:e316-e318. [PMID: 35427297 DOI: 10.1097/wno.0000000000001582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yuri Seo
- Department of Ophthalmology (YS), Institute of Vision Research, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, South Korea; Department of Ophthalmology (TYK, JH), Institute of Vision Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea; Department of Laboratory Medicine (DW, JRC, S-TL), Yonsei University College of Medicine, Seoul, South Korea; and Division of Medical Genetics (GHS), 3billion Inc, Seoul, South Korea
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Kim MR, Yoo EG, Rhie S, Seo GH, Jung MK. Growth hormone deficiency in a boy with Wiedemann-Steiner syndrome: a case report and review. Ann Pediatr Endocrinol Metab 2023; 28:S25-S28. [PMID: 35798298 PMCID: PMC10783929 DOI: 10.6065/apem.2244052.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mi Ra Kim
- Department of Pediatrics, Bundang CHA Medical Center, CHA University, Seongnam, Korea
| | - Eun-Gyong Yoo
- Department of Pediatrics, Bundang CHA Medical Center, CHA University, Seongnam, Korea
| | - Seonkyeong Rhie
- Department of Pediatrics, Bundang CHA Medical Center, CHA University, Seongnam, Korea
| | | | - Mo Kyung Jung
- Department of Pediatrics, Bundang CHA Medical Center, CHA University, Seongnam, Korea
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Tsai ASH, Kang EYC, Wang NK, Lee H, Seo GH, Khang R, Wu WC. LONG-TERM CLINICAL OUTCOMES AND GENOTYPE-PHENOTYPE CORRELATION IN FAMILIAL EXUDATIVE VITREORETINOPATHY IN A TERTIARY REFERRAL CENTER. Retina 2023; 43:1945-1950. [PMID: 37339455 DOI: 10.1097/iae.0000000000003868] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
BACKGROUND/PURPOSE To evaluate clinical outcomes and assess genotype-phenotype correlations in patients with familial exudative vitreoretinopathy (FEVR). METHODS Clinical charts of 40 patients with FEVR were reviewed. FEVR was staged per Pendergast and Trese, and retinal dragging and folds further classified per Yaguchi et al. We performed whole-exome sequencing and compared clinical characteristics between genetic-positive and genetic-negative groups. RESULTS The mean duration of follow-up was 5.4 years (range: 0.33, 15) for genetic-positive and 6.9 (range: 1, 20) for genetic-negative patients. The mean age at diagnosis was 5.6 years (0.25, 27) for genetic-positive and 6.0 (0, 32) for genetic-negative patients. Genetic-positive patients reported 100% full-term births and genetic-negative patients reported 45% full-term births ( P = 0.0012). There were more patients with retinal folds with all major vessels affected (Yaguchi's Group 4) in genetic-positive compared with genetic-negative patients (21.4% vs. 2.6%, P = 0.045). TSPAN12 was the most common (57.1%) genetic mutation in our population of which 50% exhibited asymmetric presentation. CONCLUSION Patients who test positive for a typical FEVR gene mutation reported more term births and had more severe disease by Yaguchi's classification. TSPAN12 was the most common genetic mutation in our population and had highly asymmetrical disease.
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Affiliation(s)
- Andrew S H Tsai
- Singapore National Eye Centre, Singapore
- DUKE NUS Medical School, Singapore
| | - Eugene Y C Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York; and
| | - Hane Lee
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Rin Khang
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Kim MJ, Cha S, Baek JS, Yu JJ, Seo GH, Kang M, Do HS, Lee SE, Lee BH. Genetic heterogeneity of cardiomyopathy and its correlation with patient care. BMC Med Genomics 2023; 16:270. [PMID: 37904158 PMCID: PMC10614404 DOI: 10.1186/s12920-023-01639-z] [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: 01/28/2023] [Accepted: 08/21/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Cardiomyopathy, which is a genetically and phenotypically heterogeneous pathological condition, is associated with increased morbidity and mortality. Genetic diagnosis of cardiomyopathy enables accurate phenotypic classification and optimum patient management and counseling. This study investigated the genetic spectrum of cardiomyopathy and its correlation with the clinical course of the disease. METHODS The samples of 72 Korean patients with cardiomyopathy (43 males and 29 females) were subjected to whole-exome sequencing (WES). The familial information and clinical characteristics of the patients were reviewed and analyzed according to their genotypes. RESULTS Dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), left ventricular non-compaction cardiomyopathy, and restrictive cardiomyopathy was detected in 41 (56.9%), 25 (34.7%), 4 (5.6%), and 2 (2.8%) patients, respectively. WES analysis revealed positive results in 37 (51.4%) patients. Subsequent familial testing identified ten additional familial cases. Among DCM cases, 19 (46.3%) patients exhibited positive results, with TTN variants being the most common alteration, followed by LMNA and MYH7 variants. Meanwhile, among HCM cases, 15 (60%) patients exhibited positive results with MYH7 variants being the most common alteration. In six patients with positive results, extracardiac surveillance was warranted based on disease information. The incidence of worse outcomes, such as mortality and life-threatening arrhythmic events, in patients with DCM harboring LMNA variants, was higher than that in patients with DCM harboring TTN or MYH7 variants. CONCLUSIONS Diverse genotypes were identified in a substantial proportion of patients with cardiomyopathy. Genetic diagnosis enables personalized disease surveillance and management.
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Affiliation(s)
- Mi Jin Kim
- Division of Pediatric Cardiology, Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Cha
- Division of Pediatric Cardiology, Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Suk Baek
- Division of Pediatric Cardiology, Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jeong Jin Yu
- Division of Pediatric Cardiology, Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Minji Kang
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Hyo-Sang Do
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Sang Eun Lee
- Department of Cardiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicines, Seoul, Korea.
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Ishaq T, Loid P, Ishaq HA, Seo GH, Mäkitie O, Naz S. Clinical, radiographic and molecular characterization of two unrelated families with multicentric osteolysis, nodulosis, and arthropathy. BMC Musculoskelet Disord 2023; 24:735. [PMID: 37710205 PMCID: PMC10503101 DOI: 10.1186/s12891-023-06856-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Multicentric osteolysis nodulosis and arthropathy (MONA) is a rare autosomal recessive disorder characterized by marked progressive bone loss and joint destruction resulting in skeletal deformities. MONA is caused by MMP2 deficiency. Here we report clinical and molecular analyses of four patients in two families from Pakistan and Finland. METHODS Clinical analyses including radiography were completed and blood samples were collected. The extracted DNA was subjected to whole-exome analysis or target gene sequencing. Segregation analyses were performed in the nuclear pedigree. Pathogenicity prediction scores for the selected variants and conservation analyses of affected amino acids were observed. RESULTS The phenotype in the four affected individuals was consistent with multicentric osteolysis or MONA, as the patients had multiple affected joints, osteolysis of hands and feet, immobility of knee joint and progressive bone loss. Long-term follow up of the patients revealed the progression of the disease. We found a novel MMP2 c.1336 + 2T > G homozygous splice donor variant segregating with the phenotype in the Pakistani family while a MMP2 missense variant c.1188 C > A, p.(Ser396Arg) was homozygous in both Finnish patients. In-silico analysis predicted that the splicing variant may eventually introduce a premature stop codon in MMP2. Molecular modeling for the p.(Ser396Arg) variant suggested that the change may disturb MMP2 collagen-binding region. CONCLUSION Our findings expand the genetic spectrum of Multicentric osteolysis nodulosis and arthropathy. We also suggest that the age of onset of this disorder may vary from childhood up to late adolescence and that a significant degree of intrafamilial variability may be present.
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Affiliation(s)
- Tayyaba Ishaq
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan
| | - Petra Loid
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | | | | | - Outi Mäkitie
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland.
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland.
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.
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13
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Edwards ESJ, Ojaimi S, Ngui J, Seo GH, Kim J, Chunilal S, Yablonski D, O'Hehir RE, van Zelm MC. Combined immunodeficiency and impaired PI3K signaling in a patient with biallelic LCP2 variants. J Allergy Clin Immunol 2023; 152:807-813.e7. [PMID: 37211057 DOI: 10.1016/j.jaci.2023.04.020] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Inborn errors affecting components of the T-cell receptor signaling cascade cause combined immunodeficiency with various degrees of severity. Recently, homozygous variants in LCP2 were reported to cause pediatric onset of severe combined immunodeficiency with neutrophil, platelet, and T- and B-cell defects. OBJECTIVE We sought to unravel the genetic cause of combined immunodeficiency and early-onset immune dysregulation in a 26-year-old man who presented with specific antibody deficiency, autoimmunity, and inflammatory bowel disease since early childhood. METHODS The patient was subjected to whole-exome sequencing of genomic DNA and examination of blood neutrophils, platelets, and T and B cells. Expression levels of the Src homology domain 2-containing leukocyte protein of 76 kDa (SLP76) and tonic and ligand-induced PI3K signaling were evaluated by flow-cytometric detection of phosphorylated ribosomal protein S6 in B and T cells. RESULTS Compound heterozygous missense variants were identified in LCP2, affecting the proline-rich repeat domain of SLP76 (p.P190R and p.R204W). The patient's total B- and T-cell numbers were within the normal range, as was platelet function. However, neutrophil function, numbers of unswitched and class-switched memory B cells, and serum IgA were decreased. Moreover, intracellular SLP76 protein levels were reduced in the patient's B cells, CD4+ and CD8+ T cells, and natural killer cells. Tonic and ligand-induced levels of phosphorylated ribosomal protein S6 and ligand-induced phosphorylated PLCγ1 were decreased in the patient's B cells and CD4+ and CD8+ T cells. CONCLUSIONS Biallelic variants in LCP2 impair neutrophil function and T-cell and B-cell antigen-receptor signaling and can cause combined immunodeficiency with early-onset immune dysregulation, even in the absence of platelet defects.
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Affiliation(s)
- Emily S J Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Australia; Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia
| | - Samar Ojaimi
- Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia; Monash Pathology, Monash Health, Melbourne, Australia; Monash Infectious Diseases, Monash Health, Melbourne, Australia; Monash Lung Sleep Allergy Immunology, Monash Health, Melbourne, Australia; Department of Medicine, Southern Clinical School, Monash Health and Monash University, Melbourne, Australia.
| | - James Ngui
- Monash Pathology, Monash Health, Melbourne, Australia
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc, Seoul, Korea
| | - JiHye Kim
- Division of Medical Genetics, 3billion Inc, Seoul, Korea
| | - Sanjeev Chunilal
- Department of Pathology and Radiology, Monash Health, Melbourne, Australia
| | - Deborah Yablonski
- Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Robyn E O'Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Australia; Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia; Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Alfred Hospital, Melbourne, Australia
| | - Menno C van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology, Central Clinical School, Monash University, Melbourne, Australia; Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia; Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Alfred Hospital, Melbourne, Australia.
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14
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Shafique A, Sultan T, Alzahrani F, Hun Seo G, Alkuraya FS, Naz S. Genomic Analysis of Multiplex Consanguineous Families Reveals Causes of Neurodevelopmental Disorders with Epilepsy. Gene 2023:147599. [PMID: 37393059 DOI: 10.1016/j.gene.2023.147599] [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: 03/27/2023] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
INTRODUCTION Neurodevelopmental disorders (NDD) are a diverse group of disorders that affect the development of the nervous system. Epilepsy is a common phenotypic aspect of NDD. METHODS We recruited eight consanguineous families from Pakistan which segregated recessively inherited NDD with epilepsy. Magnetic Resonance imaging (MRI) and Electroencephalogram (EEG) were completed. Exome sequencing was carried out for selected participants from each family. The exome data were analyzed for exonic and splice-site variants that had allele frequencies of less than 0.01 in public databases. RESULTS Clinical investigations determined that developmental delay, intellectual disability and seizures were manifested by most patients in early childhood. EEG findings were abnormal in the participants of four families. MRI revealed demyelination orcerebral atrophic changes in multiple participants. We identified four novel homozygous variants including nonsense andmissense variants in OCLN, ALDH7A1, IQSEC2 and COL3A1, segregating with the phenotypes in the participants of four families. Previously reported homozygous variants of CNTNAP2, TRIT1 and NARS1 were found in individuals from three families. Clinical utility was observed in directing treatment in case of patients with an ALDH7A1 variant which included pyridoxine administration and enabling accurate counseling about the natural history and recurrence risk. CONCLUSION Our results add to the clinical and molecular delineation of very rare NDD with epilepsy. The high success rate of exome sequencing is likely attributable to the expectation of homozygous variants in patients of consanguineous families, and in one case, the availability of positional mapping data that greatly aided the variant prioritization.
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Affiliation(s)
- Anum Shafique
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
| | - Tipu Sultan
- Children's Hospital & the Institute of Child Health, Lahore, Pakistan.
| | - Fatema Alzahrani
- Center for Genomic Medicine, Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | | | - Fowzan S Alkuraya
- Center for Genomic Medicine, Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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15
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Jung J, Lee JH, Seo GH, Keum C, Kang HG, Cho H, Lee H, Park SK, Baek CH, Han R, Lee ST, Cho MH, Yim HE, Koo JW, Lee BH. Genetic diagnosis of kidney disease by whole exome sequencing and its clinical application. Clin Genet 2023. [PMID: 37270787 DOI: 10.1111/cge.14382] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
The genetic spectrum of genetic kidney diseases (GKD) and the application of genetic diagnoses to patient care were assessed by whole exome sequencing (WES) of the DNA of 172 pediatric or adult patients with various kidney diseases. WES diagnosed genetic diseases in 63 (36.6%) patients. The diagnostic yields in patients with glomerulopathy were 33.8% (25/74 pts) due to variants in 10 genes, 58.8% (20/34) in patients with tubulointerstitial disease due to variants in 18 genes, 33.3% (15/45) in patients with cystic disease/ciliopathy due to variants in 10 genes, 18.2% (2/11) in patients with congenital anomalies of the kidneys and urinary tract (CAKUT) due to variants in two genes, and 12.5% (1/8) in patients with end stage kidney disease (ESKD). The diagnosis rate was high in patients aged <1-6 years (46-50.0%), and low in patients aged ≥40 years (9.1%). Renal phenotype was reclassified in 10 (15.9%) of 63 patients and clinical management altered in 10 (15.9%) of 63 patients after genetic diagnosis. In conclusion, these findings demonstrated the diagnostic utility of WES and its effective clinical application in patients, with various kinds of kidney diseases, across the different age groups.
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Affiliation(s)
- Jiwon Jung
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Joo Hoon Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Go Hun Seo
- 3billion, Inc., Seoul, Republic of Korea
| | | | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Heeyeon Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hajeong Lee
- Division of Nephrology, Department of Internal medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Su-Kil Park
- Division of Nephrology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Chung Hee Baek
- Division of Nephrology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ro Han
- Division of Nephrology, Department of Internal Medicine, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea
| | - Sang Taek Lee
- Department of Pediatrics, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Min Hyun Cho
- Department of Pediatrics, Kyungpook National University Hospital, Kyungpook National University, School of Medicine, Daegu, Republic of Korea
| | - Hyung Eun Yim
- Department of Pediatrics, Korea University Ansan Hospital, Korea University College of Medicine, Ansan-si, Republic of Korea
| | - Ja Wook Koo
- Department of Pediatrics, Inje University, College of Medicine, Sanggye Paik Hospital, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
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16
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Manzoor H, Zahid H, Emerling CA, Kumar KR, Hussain HMJ, Seo GH, Wajid M, Naz S. A biallelic variant of DCAF13 implicated in a neuromuscular disorder in humans. Eur J Hum Genet 2023; 31:629-637. [PMID: 36797467 PMCID: PMC10250411 DOI: 10.1038/s41431-023-01319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Neuromuscular disorders encompass a broad range of phenotypes and genetic causes. We investigated a consanguineous family in which multiple patients had a neuromuscular disorder characterized by a waddling gait, limb deformities, muscular weakness and facial palsy. Exome sequencing was completed on the DNA of three of the four patients. We identified a novel missense variant in DCAF13, ENST00000612750.5, NM_015420.7, c.907 G > A;p.(Asp303Asn), ENST00000616836.4, NM_015420.6, c.1363 G > A:p.(Asp455Asn) (rs1209794872) segregating with this phenotype; being homozygous in all four affected patients and heterozygous in the unaffected individuals. The variant was extremely rare in the public databases (gnomAD allele frequency 0.000007081); was absent from the DNA of 300 ethnically matched controls and affected an amino acid which has been conserved across 1-2 billion years of evolution in eukaryotes. DCAF13 contains three WD40 domains and is hypothesized to have roles in both rRNA processing and in ubiquitination of proteins. Analysis of DCAF13 with the p.(Asp455Asn) variant predicted that the amino acid change is deleterious and affects a β-hairpin turn, within a WD40 domain of the protein which may decrease protein stability. Previously, a heterozygous variant of DCAF13 NM_015420.6, c.20 G > C:p.(Trp7Ser) with or without a heterozygous missense variant in CCN3, was suggested to cause inherited cortical myoclonic tremor with epilepsy. In addition, a heterozygous DCAF13 variant has been associated with autism spectrum disorder. Our study indicates a potential role of biallelic DCAF13 variants in neuromuscular disorders. Screening of additional patients with similar phenotype may broaden the allelic and phenotypic spectrum due to DCAF13 variants.
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Affiliation(s)
- Humera Manzoor
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Hafsa Zahid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | | | - Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | | | - Muhammad Wajid
- Department of Zoology, University of Okara, Punjab, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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17
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Chang YH, Kang EYC, Liu L, Jenny LA, Khang R, Seo GH, Lee H, Chen KJ, Wu WC, Hsiao MC, Wang NK. Maternal mosaicism in SSBP1 causing optic atrophy with retinal degeneration: implications for genetic counseling. Orphanet J Rare Dis 2023; 18:131. [PMID: 37259171 PMCID: PMC10233871 DOI: 10.1186/s13023-023-02748-9] [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: 02/07/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Optic atrophy-13 with retinal and foveal abnormalities (OPA13) (MIM #165510) is a mitochondrial disease in which apparent bilateral optic atrophy is present and sometimes followed by retinal pigmentary changes or photoreceptors degeneration. OPA13 is caused by heterozygous mutation in the SSBP1 gene, associated with variable mitochondrial dysfunctions. RESULTS We have previously reported a 16-year-old Taiwanese male diagnosed with OPA13 and SSBP1 variant c.320G>A (p.Arg107Gln) was identified by whole exon sequence (WES). This variant was assumed to be de novo since his parents were clinically unaffected. However, WES and Sanger sequencing further revealed the proband's unaffected mother carrying the same SSBP1 variant with a 13% variant allele frequency (VAF) in her peripheral blood. That finding strongly indicates the maternal gonosomal mosaicism contributing to OPA13, which has not been reported before. CONCLUSIONS In summary, we described the first case of OPA13 caused by maternal gonosomal mosaicism in SSBP1. Parental mosaicism could be a serious issue in OPA13 diagnosis, and appropriate genetic counseling should be considered.
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Affiliation(s)
- Yin-Hsi Chang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Laura Liu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Laura A Jenny
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, 635 West 165th Street, New York, NY, 10032, USA
| | - Rin Khang
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc., Seoul, South Korea
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Meng-Chang Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, 635 West 165th Street, New York, NY, 10032, USA.
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18
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Chaves LD, Carvalho LML, Tolezano GC, Pires SF, Costa SS, de Scliar MO, Giuliani LDR, Bertola DR, Santos-Rebouças CB, Seo GH, Otto PA, Rosenberg C, Vianna-Morgante AM, Krepischi ACV. Skewed X-chromosome Inactivation in Women with Idiopathic Intellectual Disability is Indicative of Pathogenic Variants. Mol Neurobiol 2023; 60:3758-3769. [PMID: 36943625 DOI: 10.1007/s12035-023-03311-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
Intellectual disability (ID) is an early onset impairment in cognitive functioning and adaptive behavior, affecting approximately 1% of the population worldwide. Extreme skewing of X-chromosome inactivation (XCI) can be associated with ID phenotypes caused by pathogenic variants in the X chromosome. We analyzed the XCI pattern in blood samples of 194 women with idiopathic ID, using the androgen receptor gene (AR) methylation assay. Among the 136 patients who were informative, 11 (8%) presented with extreme or total XCI skewing (≥ 90%), which was significantly higher than expected by chance. Whole-exome data obtained from these 11 patients revealed the presence of dominant pathogenic variants in eight of them, all sporadic cases, resulting in a molecular diagnostic rate of 73% (8/11 patients). All variants were mapped to ID-related genes with dominant phenotypes: four variants in the X-linked genes DDX3X (an XCI escape gene; two cases), WDR45, and PDHA1, and four variants in the autosomal genes KCNB1, CTNNB1, YY1, and ANKRD11. Three of the autosomal genes had no obvious correlation with the observed XCI skewing. However, YY1 is a known transcriptional repressor that acts in the binding of the XIST long noncoding RNA on the inactive X chromosome, providing a mechanistic link between the pathogenic variant and the detected skewed XCI in the carrier. These data confirm that extreme XCI skewing in females with ID is highly indicative of causative X-linked pathogenic variants, and point to the possibility of identifying causative variants in autosomal genes with a XCI role.
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Affiliation(s)
- Luiza D Chaves
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Laura M L Carvalho
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Giovanna C Tolezano
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sara F Pires
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Silvia S Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marília O de Scliar
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Liane de R Giuliani
- University Hospital Maria Aparecida Pedrossian, Federal University of Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Debora R Bertola
- Unidade de Genética Do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cíntia B Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Go Hun Seo
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Paulo A Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Angela M Vianna-Morgante
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana C V Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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19
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Chang YH, Kang EYC, Liu L, Jenny LA, Khang R, Seo GH, Lee H, Chen KJ, Wu WC, Hsiao MC, Wang NK. Maternal Mosaicism in SSBP1 Causing Optic Atrophy with Retinal Degeneration: Implications for Genetic Counseling. Res Sq 2023:rs.3.rs-2554402. [PMID: 36993412 PMCID: PMC10055506 DOI: 10.21203/rs.3.rs-2554402/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Background: Optic atrophy-13 with retinal and foveal abnormalities (OPA13) (MIM #165510) is a mitochondrial disease in which apparent bilateral optic atrophy is present and sometimes followed by retinal pigmentary changes or photoreceptors degeneration. OPA13 is caused by heterozygous mutation in the SSBP1 gene, associated with variable mitochondrial dysfunctions. Results: We have previously reported a 16-year-old Taiwanese male diagnosed with OPA13 and SSBP1 variant c.320G>A (p.Arg107Gln) was identified by whole exon sequence (WES). This variant was assumed to be de novo since his parents were clinically unaffected. However, WES and Sanger sequencing further revealed the proband’s unaffected mother carrying the same SSBP1 variant with a 13% variant allele frequency (VAF) in her peripheral blood. That finding strongly indicates the maternal gonosomal mosaicism contributing to OPA13, which has not been reported before. Conclusions: In summary, we described the first case of OPA13 caused by maternal gonosomal mosaicism in SSBP1 . Parental mosaicism could be a serious issue in OPA13 diagnosis, and appropriate genetic counseling should be considered.
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20
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Park EG, Seo GH, Yang A. DHX30-Associated Neurodevelopmental Disorder with Severe Motor Impairment and Absent Language: First Korean Case in Two Siblings and Literature Review. Ann Clin Lab Sci 2023; 53:325-333. [PMID: 37094863] [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] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
DHX30 variants have recently been reported in patients with neurodevelopmental disorders with severe motor impairment and absent language (NEDMIAL). We report the first Korean siblings presenting with NEDMIAL and previously unreported clinical features harboring a rare de novo DHX30 missense variant. The proband was a 10-year-old boy presenting with intellectual disability with severe motor impairment, absent language, facial dysmorphism, strabismus, sleep disturbances, and feeding difficulties. We performed whole-exome sequencing using genomic deoxyribonucleic acid isolated from buccal swabs, which revealed a heterozygous missense variant of DHX30: (c.2344C>T, p.Arg782Trp). Sanger sequencing was conducted for the proband, the affected sister, and each parent. The same variant was confirmed in two siblings but not in their parents, suggesting the possibility of de novo germline mosaicism.
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Affiliation(s)
- Eu Gene Park
- Department of Pediatrics, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | | | - Aram Yang
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
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21
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Choi Y, Choi J, Do H, Hwang S, Seo GH, Choi IH, Keum C, Choi JH, Kang M, Kim GH, Yoo HW, Lee BH. KBG syndrome: Clinical features and molecular findings in seven unrelated Korean families with a review of the literature. Mol Genet Genomic Med 2022; 11:e2127. [PMID: 36564961 PMCID: PMC10094073 DOI: 10.1002/mgg3.2127] [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: 06/23/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND KBG syndrome is a rare genetic disorder involving macrodontia of the upper central incisors, craniofacial, skeletal, and neurologic symptoms, caused either by a heterozygous variant in ANKRD11 or deletion of 16q24.3, including ANKRD11. Diagnostic criteria were proposed in 2007 based on 50 cases, but KBG syndrome remains underdiagnosed. METHODS Whole exome sequencing (WES) and array comparative genomic hybridization (array CGH) were conducted for genetic analysis and patient phenotypes were characterized based on medical records. RESULTS Eight patients from seven unrelated families were confirmed with KBG syndrome. All patients (8/8, 100%) had some degree of craniofacial dysmorphism and developmental delay or intellectual disabilities. Triangular face, synophrys, anteverted nostril, prominent ears, long philtrum, and tented upper lip, which are typical facial dysmorphism findings in patients with KBG syndrome, were uniformly identified in the eight patients participating in this study, with co-occurrence rates of 4/8 (50%), 4/8 (50%), 4/8 (50%), 4/8 (50%), 5/8 (62.5%), and 5/8 (62.5%), respectively. Various clinical manifestations not included in the diagnostic criteria were observed. Six patients had point mutations in ANKRD11, one had an exonic deletion of ANKRD11, and one had a 16q24.3 microdeletion. According to the ACMG guidelines, all mutations were classified as pathogenic. The c.2454dup (p.Asn819fs*1) mutation in Pt 4 was reported previously. The remaining variants (c.397 + 1G>A, c.226 + 1G>A, c.2647del (p.Glu883Argfs*94), and c.4093C>T (p.Arg1365Ter)) were novel. CONCLUSION The clinical and molecular features of eight patients from seven unrelated Korean families with KBG syndrome described here will assist physicians in understanding this rare genetic condition.
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Affiliation(s)
- Yunha Choi
- Department of Pediatrics, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jungmin Choi
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hyosang Do
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Soojin Hwang
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - In Hee Choi
- Department of Genetic Counseling, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Jin-Ho Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Minji Kang
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Han-Wook Yoo
- Department of Pediatrics, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.,Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
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22
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Kim SH, Seo GH, Oh SH, Chung WY, Yu J. A Novel Nonsense Variant in the <i>BCL11A</i> Gene in a Male Patient with Intellectual Disability and Epilepsy. Ann Child Neurol 2022. [DOI: 10.26815/acn.2022.00304] [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: 12/14/2022] Open
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23
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Chen N, Lee H, Kim AH, Liu PK, Kang EYC, Tseng YJ, Seo GH, Khang R, Liu L, Chen KJ, Wu WC, Hsiao MC, Wang NK. Case report: novel PCDH15 variant causes usher syndrome type 1F with congenital hearing loss and syndromic retinitis pigmentosa. BMC Ophthalmol 2022; 22:441. [PMID: 36384460 PMCID: PMC9670441 DOI: 10.1186/s12886-022-02659-6] [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] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/29/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Usher syndrome (USH) is an autosomal recessive disorder primarily responsible for deaf-blindness. Patients with subtype Usher syndrome type 1 (USH1) typically experience congenital sensorineural hearing loss, abnormal vestibular function, and retinitis pigmentosa (RP). Here we present a case of Usher syndrome type 1F (USH1F) with a novel homozygous variant in the calcium-dependent cell-cell adhesion protocadherin-15 (PCDH15) gene.
Case presentation
Ophthalmic examinations were evaluated over a course of 10 years and the disease-causing variant was identified by whole exome sequencing (WES). Initial and follow-up examination of color fundus photos after 10 years revealed an increase in bone spicule pigment deposits in both eyes. A parafoveal hyper-AF ring in both eyes was shown in fundus autofluorescence (FAF) with a progressive diameter-wise constriction observed over 8 years. Outer nuclear layer (ONL) loss was observed in parafoveal and perifoveal regions of both eyes on spectral domain–optical coherence tomography (SD-OCT). Full-field electroretinography (ffERG) showed extinguished global retinal function. WES identified a novel two-base-pair deletion, c.60_61del (p.Phe21Ter), in the PCDH15 gene, confirming the diagnosis of USH1F.
Conclusions
We report a novel homozygous PCDH15 pathogenic variant expected to lead to nonsense-mediated decay (NMD) of PCDH15 mRNA. The patient exhibits a loss of function with USH1F, experiencing congenital hearing loss and syndromic RP.
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24
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Thomas Q, Motta M, Gautier T, Zaki MS, Ciolfi A, Paccaud J, Girodon F, Boespflug-Tanguy O, Besnard T, Kerkhof J, McConkey H, Masson A, Denommé-Pichon AS, Cogné B, Trochu E, Vignard V, El It F, Rodan LH, Alkhateeb MA, Jamra RA, Duplomb L, Tisserant E, Duffourd Y, Bruel AL, Jackson A, Banka S, McEntagart M, Saggar A, Gleeson JG, Sievert D, Bae H, Lee BH, Kwon K, Seo GH, Lee H, Saeed A, Anjum N, Cheema H, Alawbathani S, Khan I, Pinto-Basto J, Teoh J, Wong J, Sahari UBM, Houlden H, Zhelcheska K, Pannetier M, Awad MA, Lesieur-Sebellin M, Barcia G, Amiel J, Delanne J, Philippe C, Faivre L, Odent S, Bertoli-Avella A, Thauvin C, Sadikovic B, Reversade B, Maroofian R, Govin J, Tartaglia M, Vitobello A. Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huët anomaly. Am J Hum Genet 2022; 109:1909-1922. [PMID: 36044892 PMCID: PMC9606387 DOI: 10.1016/j.ajhg.2022.08.008] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
The transmembrane protein TMEM147 has a dual function: first at the nuclear envelope, where it anchors lamin B receptor (LBR) to the inner membrane, and second at the endoplasmic reticulum (ER), where it facilitates the translation of nascent polypeptides within the ribosome-bound TMCO1 translocon complex. Through international data sharing, we identified 23 individuals from 15 unrelated families with bi-allelic TMEM147 loss-of-function variants, including splice-site, nonsense, frameshift, and missense variants. These affected children displayed congruent clinical features including coarse facies, developmental delay, intellectual disability, and behavioral problems. In silico structural analyses predicted disruptive consequences of the identified amino acid substitutions on translocon complex assembly and/or function, and in vitro analyses documented accelerated protein degradation via the autophagy-lysosomal-mediated pathway. Furthermore, TMEM147-deficient cells showed CKAP4 (CLIMP-63) and RTN4 (NOGO) upregulation with a concomitant reorientation of the ER, which was also witnessed in primary fibroblast cell culture. LBR mislocalization and nuclear segmentation was observed in primary fibroblast cells. Abnormal nuclear segmentation and chromatin compaction were also observed in approximately 20% of neutrophils, indicating the presence of a pseudo-Pelger-Huët anomaly. Finally, co-expression analysis revealed significant correlation with neurodevelopmental genes in the brain, further supporting a role of TMEM147 in neurodevelopment. Our findings provide clinical, genetic, and functional evidence that bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability due to ER-translocon and nuclear organization dysfunction.
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Affiliation(s)
- Quentin Thomas
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Corresponding author
| | - Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Thierry Gautier
- University Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt,Armed Forces College of Medicine, Cairo, Egypt
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Julien Paccaud
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - François Girodon
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Biology Division, Department of Biological Hematology, Dijon Hospital, 21000 Dijon, France
| | - Odile Boespflug-Tanguy
- Université Paris Cité, UMR 1141 NeuroDiderot, Inserm, 75019 Paris, France,Service de Neuropédiatrie, reference center for leukodystrophies, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, Nantes, France,Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Aymeric Masson
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, Nantes, France,Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Eva Trochu
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Virginie Vignard
- Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Fatima El It
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Lance H. Rodan
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA,Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center, Leipzig, Germany
| | - Laurence Duplomb
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Emilie Tisserant
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK,Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK,Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Meriel McEntagart
- Medical Genetics, St George’s University Hospitals NHS FT, London SW17 0RE, UK
| | - Anand Saggar
- Medical Genetics, St George’s University Hospitals NHS FT, London SW17 0RE, UK,The Portland Hospital, 205-209 Great Portland St, London W1W 5AH, UK
| | - Joseph G. Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA,Rady Children’s Institute for Genomic Medicine, San Diego, La Jolla, CA 92093, USA
| | - David Sievert
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyunwoo Bae
- Department of Pediatrics, Asan Medical Center Children’s Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children’s Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | | | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | - Anjum Saeed
- Children’s Hospital and University of Child Health Lahore, Lahore, Pakistan
| | - Nadeem Anjum
- Children’s Hospital and University of Child Health Lahore, Lahore, Pakistan
| | - Huma Cheema
- Children’s Hospital and University of Child Health Lahore, Lahore, Pakistan
| | | | | | | | - Joyce Teoh
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A∗STAR, Singapore, Singapore
| | - Jasmine Wong
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A∗STAR, Singapore, Singapore
| | - Umar Bin Mohamad Sahari
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A∗STAR, Singapore, Singapore
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Kristina Zhelcheska
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Melanie Pannetier
- Service d’Hématologie cellulaire et hémostase bioclinique, CHU Rennes, Rennes, France
| | - Mona A. Awad
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute National Research Centre, Cairo, Egypt
| | - Marion Lesieur-Sebellin
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Giulia Barcia
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Jeanne Amiel
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Julian Delanne
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Centre de Référence maladies rares « Anomalies du Développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Centre de Référence maladies rares « Anomalies du Développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Référence Anomalies du Développement CLAD Ouest, Univ Rennes, Rennes, France,Institut de Génétique et Développement de Rennes, CNRS Inserm UMR 6290, ERL 1305, Univ Rennes, Rennes, France
| | | | - Christel Thauvin
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France,Centre de référence maladies rares « déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A∗STAR, Singapore, Singapore,Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey,Smart-Health Initiative, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jérôme Govin
- University Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France,Corresponding author
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Khan AU, Khan I, Khan MI, Latif M, Siddiqui MI, Khan SU, Htar TT, Wahid G, Ullah I, Bibi F, Khan A, Naseer MI, Seo GH, Jelani M. Whole exome sequencing identifies a novel compound heterozygous GFM1 variant underlying developmental delay, dystonia, polymicrogyria, and severe intellectual disability in a Pakhtun family. Am J Med Genet A 2022; 188:2693-2700. [PMID: 35703069 DOI: 10.1002/ajmg.a.62856] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 01/25/2023]
Abstract
Mitochondrial protein synthesis requires three elongation factors including EF-Tu (TUFM; OMIM 602389), EF-Ts (TSFM; OMIM 604723), and EF-G1 (GFM1; OMIM 606639). Pathogenic variants in any of these three members result in defective mitochondrial translation which can impart an oxidative phosphorylation (OXPHOS) deficiency. In this study, we investigated a consanguineous Pakhtun Pakistani family. There were four affected siblings at the time of this study and one affected girl had died in infancy. The index patient had severe intellectual disability, global developmental delay, dystonia, no speech development, feeding difficulties, and nystagmus. MRI brain presented thinning of corpus callosum and polymicrogyria. Whole exome sequencing revealed a novel compound heterozygous variant in GFM1 located on chromosome 3q25.32. Sanger sequencing confirmed recessive segregation of the maternal (NM_001308164.1:c.409G > A; p.Val137Met) and paternal (NM_001308164.1:c.1880G > A; p.Arg627Gln) variants in all the four affected siblings. These variants are classified as "likely-pathogenic" according to the recommendation of ACMG/AMP guideline. GFM1 alterations mostly lead to severe phenotypes and the patients may die in early neonatal life; however, four of the affected siblings had survived till the ages of 10-17 years, without developing any life-threatening conditions. Mostly, in cousin marriages, the pathogenic variants are identical-by-descent, and affected siblings born to such parents are homozygous. Three homozygous variants were shortlisted in the analysis of the WES data, but Sanger sequencing did not confirm their segregation with the disease phenotype. This is the first report from Pakistan expanding pathogenicity of GFM1 gene.
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Affiliation(s)
- Atta Ullah Khan
- Department of Medicine, Pak International Medical College Hayatabad Phase 5, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Ibrar Khan
- Rare Disease Genetics and Genomics, Centre for Omic Sciences, Khyber Pakhtunkhwa, Pakistan
| | | | - Muhammad Latif
- Centre for Genetics and Inherited Diseases (CGID), Taibah University, Madinah, Saudi Arabia
| | - Muhammad Imran Siddiqui
- Radiology Department, North West General Hospital and Research Center, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Shafi Ullah Khan
- School of Pharmacy Monash University Malaysia Jalan Lagoon Selatan Bandar Sunway 47500 Selangor, Malaysia
| | - Thet Thet Htar
- School of Pharmacy Monash University Malaysia Jalan Lagoon Selatan Bandar Sunway 47500 Selangor, Malaysia
| | - Ghazala Wahid
- Department of Radiology, Hayatabad Medical Complex, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Ikram Ullah
- International Islamic University, Sulaiman Bin Abdullah Aba Al-Khail Centre for Interdisciplinary Research in Basic Sciences, International Islamic University, Pakistan
| | - Fehmida Bibi
- Department of Medical Laboratory Technology, King Abdulaziz University, Jeddah, Saudi Arabia.,Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Imran Naseer
- Department of Medical Laboratory Technology, King Abdulaziz University, Jeddah, Saudi Arabia.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Go Hun Seo
- 3billion Inc., Seoul, Republic of Korea (South Korea)
| | - Musharraf Jelani
- Rare Disease Genetics and Genomics, Centre for Omic Sciences, Khyber Pakhtunkhwa, Pakistan
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26
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Freire BL, Homma TK, Lerario AM, Seo GH, Han H, de Assis Funari MF, Gomes NL, Rosemberg C, Krepischi ACV, de Andrade Vasques G, Malaquias AC, de Lima Jorge AA. High frequency of genetic/epigenetic disorders in short stature children born with very low birth weight. Am J Med Genet A 2022; 188:2599-2604. [PMID: 35792504 DOI: 10.1002/ajmg.a.62892] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 01/24/2023]
Abstract
Most infants born with very low birth weight (VLBW, birth weight < 1500 g) show spontaneous catch-up growth in postnatal life. The reasons for the absence of catch-up growth are not entirely understood. We performed a comprehensive investigation of 52 children born with VLBW. Ten children had a history of an external cause that explained the VLBW and five refused genetic evaluation. Twenty-three cases were initially evaluated by a candidate gene approach. Patients with a negative result in the candidate gene approach (n = 14) or without clinical suspicion (n = 14) were assessed by chromosome microarray analysis (CMA) and/or whole-exome sequencing (WES). A genetic condition was identified in 19 of 37 (51.4%) patients without an external cause, nine by candidate gene approach, and 10 by a genomic approach (CMA/WES). Silver-Russell syndrome was the most frequent diagnosis (n = 5) and the remaining patients were diagnosed with other rare monogenic conditions. Almost all patients with a positive genetic diagnosis exhibited syndromic features (94.4%). However, microcephaly, neurodevelopmental disorders, major malformation, or facial dysmorphism were also frequently observed in children with an external cause. In conclusion, a significant proportion of children born with VLBW with persistent short stature have a genetic/epigenetic condition.
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Affiliation(s)
- Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Antônio Marcondes Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Heonjong Han
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Mariana Ferreira de Assis Funari
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia, Santa Casa de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Carla Rosemberg
- Department of Genetics & Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Consolacao, Brazil
| | | | - Gabriela de Andrade Vasques
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Alexsandra Christianne Malaquias
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia Pediátrica, Departamento de Pediatria, Irmandade da Santa Casa de Misericórdia de São Paulo, Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, Consolacao, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
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Moosa S, Coetzer KC, Lee E, Seo GH. Undiagnosed disease program in South Africa: Results from first 100 exomes. Am J Med Genet A 2022; 188:2684-2692. [PMID: 35616356 PMCID: PMC10947569 DOI: 10.1002/ajmg.a.62847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 02/07/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023]
Abstract
The Undiagnosed Disease Program in South Africa (UDP) sought to prospectively evaluate the clinical utility of exome sequencing (ES) in a phenotypically diverse, multi-ethnic cohort of South African patients with suspected rare genetic disorders. ES was undertaken in 100 sequential patients (93 singletons, 3 duos, and 4 trios) recruited to the UDP at Stellenbosch University. The data were analyzed through two separate bioinformatics pipelines (EVIDENCE from 3 billion and our in-house pipeline). A definitive diagnosis could be reached in 51% (51/100) patients, with 46% (46/100) patients having either pathogenic or likely pathogenic single-nucleotide variants/indels (SNVs/indels), and 5 patients with likely-pathogenic copy number variants (CNVs) (5/100). The CNVs were subsequently confirmed on microarray or MLPA analysis. Detailed phenotyping and HPO terms enabled analysis and variant identification. Twenty-five novel variants in 22 genes are reported here. We provide data from the first year of this UDP and show that even amongst mainly singletons from an understudied, diverse African population, ES is a valuable diagnostic tool, especially if it includes CNV analysis. The remaining undiagnosed patients present a unique opportunity for further research and novel gene discovery.
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Affiliation(s)
- Shahida Moosa
- Division of Molecular Biology and Human GeneticsStellenbosch UniversityCape TownSouth Africa
- Medical GeneticsTygerberg HospitalCape TownSouth Africa
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Kim SY, Kim BJ, Oh DY, Han JH, Yi N, Kim NJ, Park MK, Keum C, Seo GH, Choi BY. Improving genetic diagnosis by disease-specific, ACMG/AMP variant interpretation guidelines for hearing loss. Sci Rep 2022; 12:12457. [PMID: 35864128 PMCID: PMC9304357 DOI: 10.1038/s41598-022-16661-x] [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: 08/04/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022] Open
Abstract
The 2018 Hearing Loss Expert Panel (HL-EP)-specific guidelines specified from the universal 2015 ACMG/AMP guidelines are proposed to be used in genetic HL, which prompted this study. A genetic HL cohort comprising 135 unrelated probands with available exome sequencing data was established. Overall, 169 variants were prioritized as candidates and interpreted using the 2015 ACMG/AMP and 2018 HL-EP guidelines. Changes in rule application and variant classification between the guidelines were compared. The concordance rate of variant classification of each variant between the guidelines was 71.60%, with significant difference. The proportion of pathogenic variants increased from 13.02% (2015) to 29.59% (2018). Variant classifications of autosomal recessive (AR) variants that previously belonged to VUS or likely pathogenic in the 2015 guidelines were changed toward pathogenic in the 2018 guidelines more frequently than those of autosomal dominant variants (29.17% vs. 6.38%, P = 0.005). Stratification of the PM3 and PP1 rules in the 2018 guidelines led to more substantial escalation than that in the 2015 guidelines. We compared the disease-specific guidelines (2018) with the universal guidelines (2015) using real-world data. Owing to the sophistication of case-level data, the HL-specific guidelines have more explicitly classified AR variants toward "likely pathogenic" or "pathogenic", serving as potential references for other recessive genetic diseases.
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Affiliation(s)
- So Young Kim
- grid.410886.30000 0004 0647 3511Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Bong Jik Kim
- grid.254230.20000 0001 0722 6377Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Doo Yi Oh
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Hee Han
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Yi
- grid.254230.20000 0001 0722 6377Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Daejeon, South Korea ,grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Namju Justin Kim
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Moo Kyun Park
- grid.31501.360000 0004 0470 5905Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, South Korea
| | | | | | - Byung Yoon Choi
- grid.412480.b0000 0004 0647 3378Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
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29
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Choi IH, Seo GH, Park J, Kim YM, Cheon CK, Kim YM, Oh A, Byeon JH, Kang E, Shin YL, Lee JE, Kim SJ, Yu HJ, Kim WJ, Choi BY, Kim BJ, Kim YH, Im GJ, Lee HJ, Kim HJ, Han SH, Lee BH, Eun BL. Evaluation of users' level of satisfaction for an artificial intelligence-based diagnostic program in pediatric rare genetic diseases. Medicine (Baltimore) 2022; 101:e29424. [PMID: 35838999 DOI: 10.1097/md.0000000000029424] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The artificial intelligence (AI)-based genetic diagnostic program has been applied to genome sequencing to facilitate the diagnostic process. The objective of the current study was to evaluate the experience and level of satisfaction of participants using an AI-based diagnostic program for rare pediatric genetic diseases. The patients with neurodevelopmental disorders or hearing impairments, their guardians, and their physicians from 16 tertiary general hospitals were enrolled. The study period was from April 2020 to March 2021. A survey was designed to assess their experience and level of satisfaction. A total of 30 physicians and 243 patients and guardians (199 neurodevelopmental disorders and 44 hearing impairments) completed the survey. DNA samples of the subjects were collected through buccal swabs or blood collection: 211 subjects (86.8%) through buccal swab and 29 subjects (11.9%) through blood collection. Average turnaround time for result receipt was 57.54 ± 32.42 days. For the sampling method, 193 patients and guardians (81.1%) and 28 physicians (93.3%) preferred buccal swab. The level of satisfaction of the 2 groups participating in the AI-based diagnostic program was 8.31 ± 1.71 out of 10 in the patient and guardian group and 8.42 ± 1.23 in the physician group. Clinicians, patients, and guardians are satisfied with the AI-based diagnostic program in general. With an increase in AI-based precision medicine solutions, the evaluation of the user's satisfaction with appropriate provision will help improve personal health care.
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Affiliation(s)
- In Hee Choi
- Department of Genetic Counseling, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - JeongYun Park
- Department of Clinical Nursing, University of Ulsan, Seoul, South Korea
| | - Yoon-Myung Kim
- Department of Pediatrics, Gangneung Asan Hospital, College of Medicine, University of Ulsan, Gangneung, South Korea
| | - Chong Kun Cheon
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Pusan National University School of Medicine, Pusan National University Children's Hospital, South Korea
| | - Yoo-Mi Kim
- Department of Pediatrics, Pediatric Center, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Sejong, South Korea
| | - Arum Oh
- Department of Pediatrics, Chungbuk National University Hospital, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Jung Hye Byeon
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
| | - Eungu Kang
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
| | - Young-Lim Shin
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea
| | - Ji Eun Lee
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Su Jin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Hee Joon Yu
- Department of Pediatrics, Hallym University Sacred Heart Hospital, Gyeonggi-do, South Korea
| | - Woo Jin Kim
- EONE Laboratories, Harmony-ro, Yeonsu-gu, Incheon, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University College of Medicine, Chungnam National University Sejong Hospital, Sejong, South Korea
| | - Young Ho Kim
- Department of Otorhinolaryngology, Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Gi Jung Im
- Department of Otorhinolaryngology, Korea University College of Medicine, Seoul, South Korea
| | - Hyo-Jeong Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University College of Medicine, Chuncheon, South Korea
| | - Hyun Ji Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Inha University College of Medicine, Incheon, South Korea
| | - Se-Hee Han
- Korea University Guro Hospital, Seoul, South Korea
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Baik-Lin Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
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30
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Jaffal L, Akhdar H, Joumaa H, Ibrahim M, Chhouri Z, Assi A, Helou C, Lee H, Seo GH, Joumaa WH, El Shamieh S. Novel Missense and Splice Site Mutations in USH2A, CDH23, PCDH15, and ADGRV1 Are Associated With Usher Syndrome in Lebanon. Front Genet 2022; 13:864228. [PMID: 35651951 PMCID: PMC9149366 DOI: 10.3389/fgene.2022.864228] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study was to expand the mutation spectrum by searching the causative mutations in nine Lebanese families with Usher syndrome (USH) using whole-exome sequencing. The pathogenicity of candidate mutations was first evaluated according to their frequency, conservation, and in silico prediction tools. Then, it was confirmed via Sanger sequencing, followed by segregation analysis. Finally, a meta-analysis was conducted to calculate the prevalence of USH genes in the Lebanese population. Three missense mutations, two splice site mutations, and one insertion/deletion were detected in eight of the families. Four of these variants were novel: c.5535C > A; p.(Asn1845Lys) in exon 41 of CDH23, c.7130G > A; p.(Arg2377Gln) in exon 32 of ADGRV1, c.11390-1G > A in USH2A, and c.3999–6A > G in PCDH15. All the identified mutations were shown to be likely disease-causing through our bioinformatics analysis and co-segregated with the USH phenotype. The mutations were classified according to the ACMG standards. Finally, our meta-analysis showed that the mutations in ADGRV1, USH2A, and CLRN1 are the most prevalent and responsible for approximately 75% of USH cases in Lebanon. Of note, the frequency USH type 3 showed a relatively high incidence (23%) compared to the worldwide prevalence, which is around 2–4%. In conclusion, our study has broadened the mutational spectrum of USH and showed a high heterogeneity of this disease in the Lebanese population.
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Affiliation(s)
- Lama Jaffal
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Hanane Akhdar
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Hawraa Joumaa
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Zahraa Chhouri
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Alexandre Assi
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut, Lebanon
| | - Charles Helou
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut, Lebanon
| | - Hane Lee
- Rare Genetic Disease Research Center, 3billion Inc, Seoul, South Korea
| | - Go Hun Seo
- Rare Genetic Disease Research Center, 3billion Inc, Seoul, South Korea
| | - Wissam H Joumaa
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Said El Shamieh
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
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Abstract
The complex and evolving nature of clinical phenotypes have made genetically diagnosing pediatric patients with movement disorders difficult. Here, we describe this diverse complexity in the clinical and genetic features of a pediatric cohort examined by whole-exome sequencing (WES) and demonstrate the clinical benefit of WES as a diagnostic tool in a pediatric cohort. We evaluated 75 patients with diverse single or combined movement phenomenologies using WES. WES identified 42 variants in 37 genes (56.0%). The detection rate was highest in patients with dystonia (11/13, 84.6%), followed by ataxia (21/38, 55.3%), myoclonus (3/6, 50.0%), unspecified dyskinesia (1/4, 25.0%), tremor (1/1, 100%), respectively. Most genetically diagnosed patients (90.5%) were affected by other neurologic or systemic manifestations; congenital hypotonia (66.7%), and epilepsy (42.9%) were the most common phenotypes. The genetic diagnosis changed the clinical management for five patients (6.7%), including treatments targeting molecular abnormalities, and other systemic surveillance such as cancer screening. Early application of WES yields a high diagnostic rate in pediatric movement disorders, which can overcome the limitations of the traditional phenotype-driven strategies due to the diverse phenotypic and genetic complexity. Additionally, this early genetic diagnosis expands the patient’s clinical spectrum and provides an opportunity for tailored treatment.
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Affiliation(s)
- Min-Jee Kim
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine, Seoul, South Korea
| | - Mi-Sun Yum
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine, Seoul, South Korea
- *Correspondence: Mi-Sun Yum, ; Beom Hee Lee,
| | | | - Tae-Sung Ko
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine, Seoul, South Korea
| | - Beom Hee Lee
- Department of Genetics, Asan Medical Center, Ulsan University College of Medicine, Seoul, South Korea
- *Correspondence: Mi-Sun Yum, ; Beom Hee Lee,
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Chang YH, Kang EYC, Liu PK, Levi SR, Wang HH, Tseng YJ, Seo GH, Lee H, Yeh LK, Chen KJ, Wu WC, Lai CC, Liu L, Wang NK. Photoreceptor Manifestations of Primary Mitochondrial Optic Nerve Disorders. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 35506936 PMCID: PMC9078049 DOI: 10.1167/iovs.63.5.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Indexed: 12/23/2022] Open
Abstract
Purpose To compare the manifestations of photoreceptors (PRs) in three hereditary optic neuropathies affected by primary mitochondrial dysfunction and discuss whether the retinal ganglion cells (RGCs) or the PRs are preferentially affected. Methods A retrospective analysis of patients with genetically confirmed diagnoses of optic neuropathies associated with mitochondrial dysfunction was performed. This cohort included Leber's hereditary optic neuropathy (LHON), autosomal dominant optic atrophy type 1 (OPA1), and optic atrophy type 13 (OPA13). Patient chart evaluations included clinical characteristics, best-corrected visual acuity (BCVA), fundus photography, spectral-domain optical coherence tomography (SD-OCT), electroretinogram (ERG), and visual evoked potential data. Results This analysis included seven patients with LHON, six with OPA1, and one with OPA13 from a tertiary medical center. Thirteen of the 14 individuals were male. The average BCVA at diagnosis was 20/285 and 20/500 in the right and left eyes, respectively. Five of the seven patients with LHON, and three of the six patients with OPA1 also showed a mild amplitude reduction or delayed latency on light-adapted ERG and 30-Hz flicker responses; however, SD-OCT imaging did not show correlated PR abnormalities. Notably, a 7-year follow-up of a patient with OPA13 revealed degeneration of RGCs prior to the degeneration of PRs. Follow-up data also demonstrated continuous loss of cone outer segment tips on SD-OCT imaging. Conclusions RGCs are, in general, affected by mitochondrial dysfunction, whereas variable PR dysfunction exists in patients with LHON and OPA1, especially with respect to the cone responses. Involvement of PRs is particularly evident in OPA13 after RGC degenerations.
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Affiliation(s)
- Yin-Hsi Chang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Pei-Kang Liu
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York, United States
| | - Sarah R Levi
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York, United States
| | - Hung-Hsuan Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York, United States
| | - Yun-Ju Tseng
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York, United States
| | - Go Hun Seo
- Division of Medical Genetics, 3billion, Inc., Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3billion, Inc., Seoul, South Korea
| | - Lung-Kun Yeh
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Jen Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chi-Chun Lai
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Laura Liu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,School of Traditional Chinese Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York, United States
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Ahn JH, Oh SH, Park JK, Kim KH, Lee JE, Chung WY, Lee KS, Seo GH, Lee BL. A Novel Frameshift CASK Variant in a 6-Month-Old Korean Female Infant with Global Developmental Delay, Progressive Microcephaly, and Pontocerebellar Hypoplasia: A Case Report. Ann Clin Lab Sci 2022; 52:488-493. [PMID: 35777792] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pontocerebellar hypoplasia is a heterogeneous group of rare genetic neurodevelopmental disorders marked by early degeneration of the cerebellum and brainstem. Intellectual developmental disorder with microcephaly and pontine and cerebellar hypoplasia (MICPCH; MIM#300749) is a disorder caused by pathogenic loss-of-function variants in CASK CASK gene plays a critical role in brain development by controlling neuronal development and synapse formation. This report describes a 6-month-old Korean female infant with global developmental delay, sensorineural hearing loss, axial hypotonia with hypertonia of extremities, progressive microcephaly, and pontocerebellar hypoplasia. On whole exome sequencing, the patient had a novel heterozygous frameshift CASK variant, NM_003688.3:c.535del (NP_003679.2:p. Arg179Valfs*22). This report highlights the importance of considering CASK pathogenic variants in patients with global developmental delay, progressive microcephaly, and pontocerebellar hypoplasia and the genotype-phenotype relationships.
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Affiliation(s)
- Jeong Ho Ahn
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan
| | - Ji Kyoung Park
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Kwang Hoon Kim
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Jeong Eun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Keun Soo Lee
- Department of Neurosurgery, Busan Paik Hospital, Inje University College of Medicine, Busan
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, Korea
| | - Bo Lyun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan
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Ha DJ, Park J, Seo GH, Lee K, Kwon YS, Lee JE, Kim SJ. Case Report: Infantile Cerebellar-Retinal Degeneration With Compound Heterozygous Variants in ACO2 Gene-Long-Term Follow-Up of a Sibling. Front Genet 2022; 13:729980. [PMID: 35368710 PMCID: PMC8965713 DOI: 10.3389/fgene.2022.729980] [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: 06/24/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Infantile cerebellar-retinal degeneration (ICRD) is an extremely rare, infantile-onset neuro-degenerative disease, characterized by autosomal recessive inherited, global developmental delay (GDD), progressive cerebellar and cortical atrophy, and retinal degeneration. In 2012, a biallelic pathogenic variant in ACO2 gene (NM_001098.3) was found to be causative of this disease. To date, approximately 44 variants displaying various clinical features have been reported. Here, we report a case of two siblings with compound heterozygous variants in the ACO2 gene. Two siblings without perinatal problems were born to healthy non-consanguineous Korean parents. They showed GDD and seizures since infancy. Their first brain magnetic resonance imaging (MRI), electroencephalography, and metabolic workup revealed no abnormal findings. As they grew, they developed symptoms including ataxia, dysmetria, poor sitting balance, and myopia. Follow-up brain MRI findings revealed atrophy of the cerebellum and optic nerve. Through exome sequencing of both siblings and their parents, we identified the following compound heterozygous variants in the ACO2: c.85C > T (p.Arg29Trp) and c.2303C > A (p.Ala768Asp). These two variants were categorized as likely pathogenic based on ACMG/AMP guidelines. In conclusion, this case help to broaden the genetic and clinical spectrum of the ACO2 variants associated with ICRD. We have also documented the long-term clinical course and serial brain MRI findings for two patients with this extremely rare disease.
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Affiliation(s)
- Dong Jun Ha
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea
| | - Jisun Park
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea.,Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| | | | | | - Young Se Kwon
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea.,Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| | - Ji Eun Lee
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea.,Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| | - Su Jin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, South Korea.,Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
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Seo GH, Lee J, Han H, Cho YK, Kim M, Choi Y, Rhie S, Kim YM, Cheon CK, Kim SJ, Lee J, Kang E, Yu HJ, Shin YL, Byeon JH, Yum MS, Lee BH, Eun BL. eP239: Diagnostic performance of automated streamlined, daily updated, exome analysis in patients with delayed development. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.274] [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: 11/24/2022] Open
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Son JS, Seo GH, Kim YM, Kim GH, Jin HK, Bae JS, Im HJ, Yoo HW, Lee BH. Clinical and genetic features of four patients with Pearson syndrome: An observational study. Medicine (Baltimore) 2022; 101:e28793. [PMID: 35119049 PMCID: PMC8812667 DOI: 10.1097/md.0000000000028793] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/20/2022] [Indexed: 01/04/2023] Open
Abstract
Pearson syndrome (PS) is a multisystem mitochondrial cytopathy arising from deletions in mitochondrial DNA. Pearson syndrome is a sporadic disease that affects the hematopoietic system, pancreas, eyes, liver, and heart and the prognosis is poor. Causes of morbidity include metabolic crisis, bone marrow dysfunction, sepsis, and liver failure in early infancy or childhood. Early diagnosis may minimize complications, but suspicion of the disease is difficult and only mitochondrial DNA gene testing can identify mutations. There is no specific treatment for PS, which remains supportive care according to symptoms; however, hematopoietic stem cell transplantation may be considered in cases of bone marrow failure.We herein describe the clinical and genetic characteristics of four patients with PS. One patient presented with hypoglycemia, two developed pancytopenia, and the final patient had hypoglycemia and acute hepatitis as the primary manifestation. All patients had lactic acidosis. Additionally, all patients showed a variety of clinical features including coagulation disorder, pancreatic, adrenal, and renal tubular insufficiencies. Two patients with pancytopenia died in their early childhood. Our experience expands the phenotypic spectrum associated with PS and its clinical understanding.
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Affiliation(s)
- Ji Soo Son
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Yoon-Myung Kim
- Department of Pediatrics, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, South Korea
| | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hee Kyung Jin
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae-sung Bae
- Department of Physiology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Ho Joon Im
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Han-Wook Yoo
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, South Korea
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Kim BJ, Jeon H, Lee SY, Yi N, Han JH, Seo GH, Oh SH, Choi BY. Major Contribution of GREB1L Alterations to Severe Inner Ear Malformation Largely in a Non-mendelian Fashion. Clin Exp Otorhinolaryngol 2022; 15:115-118. [PMID: 35012281 PMCID: PMC8901951 DOI: 10.21053/ceo.2021.01935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/20/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Sejong, Korea
| | - Hyoungwon Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Nayoung Yi
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Sejong, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | | | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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Sung Park J, Hun Seo G, Choi Y, Hwang S, Kang M, Do HS, Kim YH, Jin Yu J, Ai-Rhan Kim E, Jung E, Sop Lee B, Suk Baek J, Hee Lee B. Factors Affecting the Genetic Diagnostic Rate in Congenital Heart Disease. CONGENIT HEART DIS 2022. [DOI: 10.32604/chd.2022.021580] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chung EJ, You E, Oh SH, Seo GH, Chung WY, Kim YJ, Kim SJ. The First Korean Family With Boucher-Neuhäuser Syndrome Carrying a Novel Mutation in PNPLA6. J Clin Neurol 2022; 18:233-234. [PMID: 35274841 PMCID: PMC8926775 DOI: 10.3988/jcn.2022.18.2.233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Eun Joo Chung
- Department of Neurology, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
- Dementia and Neurodegenerative Disease Research Center, Inje University, Gimhae, Korea
| | - Eunkyoung You
- Department of Laboratory Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | | | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
- Rare Disease Busan Regional Center, Busan, Korea
| | - Yun Joong Kim
- Department of Neurology, Yongin Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Jin Kim
- Department of Neurology, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
- Dementia and Neurodegenerative Disease Research Center, Inje University, Gimhae, Korea
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Chiu N, Lee W, Liu PK, Levi SR, Wang HH, Chen N, Kang EYC, Seo GH, Lee H, Liu L, Wu WC, Tsai SH, Wang NK. A homozygous in-frame duplication within the LRRCT consensus sequence of CFAP410 causes cone-rod dystrophy, macular staphyloma and short stature. Ophthalmic Genet 2021; 43:378-384. [PMID: 34915818 DOI: 10.1080/13816810.2021.2010773] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ciliopathies are a group of genetic dystrophies causing syndromic and non-syndromic retinal degeneration. We identified CFAP410 as the causative gene in a patient with childhood-onset retinal dystrophy without other systemic symptoms at the age of 20. This 20-year-old man presented with cone-rod dystrophy and CFAP410 homozygous in-frame duplication variants (c.340_351dup). His clinical features included early subnormal vision, posterior pole staphyloma, and short stature. Unlike the previously reported features of retinal ciliopathy, our patient showed no obvious retinal pigmentation and only a slight hyper-autofluorescent parafoveal ring at the 16-year follow up. This case report aims to characterize the clinical features in a patient with novel, homozygous and likely pathogenic in-frame duplication variants in the CFAP410 gene. Ultimately, this report will help contribute to the understanding of CFAP410-associated ciliopathies.
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Affiliation(s)
- Ning Chiu
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, New York, USA.,Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pei-Kang Liu
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA.,Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Sarah R Levi
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Hung-Hsi Wang
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Nelson Chen
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eugene Yu-Chuan Kang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Laura Liu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wei-Chi Wu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shawn H Tsai
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, Taiwan.,Department of Optometry, Chung Shan Medical University, Taichung, Taiwan.,Department of Optometry, Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Nan-Kai Wang
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
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Lee Y, Choi Y, Seo GH, Kim GH, Keum C, Kim YM, Do HS, Choi J, Choi IH, Yoo HW, Lee BH. Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea. BMC Med Genomics 2021; 14:254. [PMID: 34706719 PMCID: PMC8555129 DOI: 10.1186/s12920-021-01104-9] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
Background The switch/sucrose nonfermenting (SWI/SNF) complex is an adenosine triphosphate-dependent chromatin-remodeling complex associated with the regulation of DNA accessibility. Germline mutations in the components of the SWI/SNF complex are related to human developmental disorders, including the Coffin–Siris syndrome (CSS), Nicolaides–Baraitser syndrome (NCBRS), and nonsyndromic intellectual disability. These disorders are collectively referred to as SWI/SNF complex-related intellectual disability disorders (SSRIDDs). Methods Whole-exome sequencing was performed in 564 Korean patients with neurodevelopmental disorders. Twelve patients with SSRIDDs (2.1%) were identified and their medical records were retrospectively analyzed. Results ARID1B, found in eight patients, was the most frequently altered gene. Four patients harbored pathogenic variants in SMARCA4, SMARCB1, ARID2, and SMARCA2. Ten patients were diagnosed with CSS, and one patient without a typical phenotype was diagnosed with ARID1B-related nonsyndromic intellectual disability. Another patient harboring the SMARCA2 pathogenic variant was diagnosed with NCBRS. All pathogenic variants in ARID1B were truncating, whereas variants in SMARCA2, SMARCB1, and SMARCA4 were nontruncating (missense). Frequently observed phenotypes were thick eyebrows (10/12), hypertrichosis (8/12), coarse face (8/12), thick lips (8/12), and long eyelashes (8/12). Developmental delay was observed in all patients, and profound speech delay was also characteristic. Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12). Conclusions SSRIDDs have a broad disease spectrum, including NCBRS, CSS, and ARID1B-related nonsyndromic intellectual disability. Thus, SSRIDDs should be considered as a small but important cause of human developmental disorders.
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Affiliation(s)
- Yena Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Yunha Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | | | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Yoo-Mi Kim
- Department of Pediatrics, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Sejong, Republic of Korea
| | - Hyo-Sang Do
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Jeongmin Choi
- Genome Research Center for Birth Defects and Genetic Diseases, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - In Hee Choi
- Department of Genetic Counseling, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Han-Wook Yoo
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.,Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea. .,Medical Genetics Center, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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42
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Lee DA, Jun KR, Lee JH, Chung WY, Seo GH, Park KM. Hypomagnesemia and seizures in a patient with an SOS1 mutation. Seizure 2021; 92:234-235. [PMID: 34607272 DOI: 10.1016/j.seizure.2021.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022] Open
Affiliation(s)
- Dong Ah Lee
- Department of Neurology, Haeundae Paik Hospital, Inje University College of Medicine, Busan, South Korea
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, South Korea
| | - Jun Ho Lee
- Department of Neurology, Haeundae Paik Hospital, Inje University College of Medicine, Busan, South Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, South Korea
| | - Go Hun Seo
- 3billion Inc., 416 Teheran-ro, Dachi-dong, Gangnam-Gu, Seoul, South Korea
| | - Kang Min Park
- Department of Neurology, Haeundae Paik Hospital, Inje University College of Medicine, Busan, South Korea.
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Kim SY, Lee S, Seo GH, Kim BJ, Oh DY, Han JH, Park MK, Lee SM, Kim B, Yi N, Kim NJ, Koh DH, Hwang S, Keum C, Choi BY. Powerful use of automated prioritization of candidate variants in genetic hearing loss with extreme etiologic heterogeneity. Sci Rep 2021; 11:19476. [PMID: 34593925 PMCID: PMC8484668 DOI: 10.1038/s41598-021-99007-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
Variant prioritization of exome sequencing (ES) data for molecular diagnosis of sensorineural hearing loss (SNHL) with extreme etiologic heterogeneity poses a significant challenge. This study used an automated variant prioritization system (“EVIDENCE”) to analyze SNHL patient data and assess its diagnostic accuracy. We performed ES of 263 probands manifesting mild to moderate or higher degrees of SNHL. Candidate variants were classified according to the 2015 American College of Medical Genetics guidelines, and we compared the accuracy, call rates, and efficiency of variant prioritizations performed manually by humans or using EVIDENCE. In our in silico panel, 21 synthetic cases were successfully analyzed by EVIDENCE. In our cohort, the ES diagnostic yield for SNHL by manual analysis was 50.19% (132/263) and 50.95% (134/263) by EVIDENCE. EVIDENCE processed ES data 24-fold faster than humans, and the concordant call rate between humans and EVIDENCE was 97.72% (257/263). Additionally, EVIDENCE outperformed human accuracy, especially at discovering causative variants of rare syndromic deafness, whereas flexible interpretations that required predefined specific genotype–phenotype correlations were possible only by manual prioritization. The automated variant prioritization system remarkably facilitated the molecular diagnosis of hearing loss with high accuracy and efficiency, fostering the popularization of molecular genetic diagnosis of SNHL.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,R&D Center, ENCell Co. Ltd, Seoul, Republic of Korea
| | - Go Hun Seo
- 3billion, Inc., Seoul, Republic of Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Nayoung Yi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Namju Justin Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Doo Hyun Koh
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea.,Department of Pathology, CHA University, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | | | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
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Yun U, Lee SA, Choi WA, Kang SW, Seo GH, Lee JH, Park G, Lee S, Choi YC, Park HJ. Clinical and genetic spectra in patients with dystrophinopathy in Korea: A single-center study. PLoS One 2021; 16:e0255011. [PMID: 34297739 PMCID: PMC8301650 DOI: 10.1371/journal.pone.0255011] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/07/2021] [Indexed: 01/16/2023] Open
Abstract
Dystrophinopathy is a group of inherited phenotypes arising from pathogenic variants in DMD. We evaluated the clinical and genetic characteristics of Korean patients with genetically confirmed dystrophinopathy. We retrospectively reviewed medical records (January 2004-September 2020) from the myopathy database maintained at the study hospital and found 227 patients from 218 unrelated families with dystrophinopathy. Clinical phenotypes included 120 (53%) Duchenne muscular dystrophy (DMD) cases, 20 (9%) intermediate phenotype muscular dystrophy (IMD) cases, 65 (29%) Becker muscular dystrophy (BMD) cases, 18 (8%) undetermined phenotypes, and 4 (2%) symptomatic carriers. The median ages at symptom onset and diagnosis were 5.0 years (interquartile range [IQR]: 3.8–8.0) and 12.0 years (IQR: 7.0–21.0), respectively. Total manual muscle test (MMT) scores decreased annually in patients with DMD, IMD, and BMD. Overall, when age increased by 1 year, total MMT scores decreased on average by -1.978, -1.681, and -1.303 in patients with DMD (p<0.001), IMD (p<0.001), and BMD (p<0.001), respectively. Exonic deletion and duplication were reported in 147 (67%) and 31 (14%) of the 218 unrelated probands, respectively. A total of 37 different small sequence variants were found in 40 (18%) of the 218 probands. The reading frame rule was applicable to 142 (94%) of the 151 probands. The present results highlight the long-term natural history and genetic spectrum of dystrophinopathy in a large-scale Korean cohort.
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Affiliation(s)
- UnKyu Yun
- Department of Neurology, Bucheon Sejong Hospital, Bucheon, Korea
| | - Seung-Ah Lee
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Ah Choi
- Department of Rehabilitation, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seong-Woong Kang
- Department of Rehabilitation, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3billion, Inc. Seoul, Republic of Korea
| | - Jung Hwan Lee
- Department of Neurology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Goeun Park
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sujee Lee
- Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young-Chul Choi
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Jun Park
- Department of Neurology, Rehabilitation Institute of Neuromuscular Disease, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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Park J, Ha DJ, Seo GH, Maeng S, Kang SM, Kim S, Lee JE. Empty Sella Syndrome Associated with Growth Hormone Deficiency: the First Case Report of Weiss-Kruszka Syndrome. J Korean Med Sci 2021; 36:e133. [PMID: 33975400 PMCID: PMC8111047 DOI: 10.3346/jkms.2021.36.e133] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/11/2021] [Indexed: 11/20/2022] Open
Abstract
Weiss-Kruszka syndrome (WSKA), caused by heterozygous loss-of-function variants in ZNF462 gene, is a recently described and extremely rare genetic disorder. The main phenotypes include characteristic craniofacial features, ptosis, dysgenesis of the corpus callosum, and neurodevelopmental impairment. We report the first Korean boy with molecularly confirmed WSKA presenting with an atypical manifestation. A 16-year-old boy with a history of bilateral ptosis surgery presented with short stature (-3.49 standard deviation score) and delayed puberty. The patient showed characteristic craniofacial features including an inverted triangular-shaped head, exaggerated Cupid's bow, arched eyebrows, down-slanting palpebral fissures, and poorly expressive face. He had a mild degree of intellectual disability and mild hypotonia. Endocrine studies in the patient demonstrated complete growth hormone deficiency (GHD) associated with empty sella syndrome (ESS), based on a magnetic resonance imaging study for the brain that showed a flattened pituitary gland and cerebrospinal fluid space herniated into the sella turcica. To identify the genetic cause, we performed whole exome sequencing (WES). Through WES, a novel de novo heterozygous nonsense variant, c.4185del; p.(Met1396Ter) in ZNF462 was identified. This is the first case of WSKA accompanied by primary ESS associated with GHD. More clinical and functional studies are needed to elucidate this association.
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Affiliation(s)
- Jisun Park
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
| | - Dong Jun Ha
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | | | - Seri Maeng
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
- Department of Psychiatry, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Sung Mo Kang
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea
- Department of Ophthalmology, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Sujin Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea.
| | - Ji Eun Lee
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
- Northwest Gyeonggi Regional Center for Rare Disease, Inha University Hospital, Incheon, Korea.
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Lee Y, Kim T, Lee M, So S, Karagozlu MZ, Seo GH, Choi IH, Lee PCW, Kim CJ, Kang E, Lee BH. De Novo Development of mtDNA Deletion Due to Decreased POLG and SSBP1 Expression in Humans. Genes (Basel) 2021; 12:genes12020284. [PMID: 33671400 PMCID: PMC7922481 DOI: 10.3390/genes12020284] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
Defects in the mitochondrial genome (mitochondrial DNA (mtDNA)) are associated with both congenital and acquired disorders in humans. Nuclear-encoded DNA polymerase subunit gamma (POLG) plays an important role in mtDNA replication, and proofreading and mutations in POLG have been linked with increased mtDNA deletions. SSBP1 is also a crucial gene for mtDNA replication. Here, we describe a patient diagnosed with Pearson syndrome with large mtDNA deletions that were not detected in the somatic cells of the mother. Exome sequencing was used to evaluate the nuclear factors associated with the patient and his family, which revealed a paternal POLG mutation (c.868C > T) and a maternal SSBP1 mutation (c.320G > A). The patient showed lower POLG and SSBP1 expression than his healthy brothers and the general population of a similar age. Notably, c.868C in the wild-type allele was highly methylated in the patient compared to the same site in both his healthy brothers. These results suggest that the co- deficient expression of POLG and SSBP1 genes could contribute to the development of mtDNA deletion.
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Affiliation(s)
- Yeonmi Lee
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (Y.L.); (M.L.); (S.S.); (M.Z.K.)
| | - Taeho Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.K.); (G.H.S.); (I.H.C.)
| | - Miju Lee
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (Y.L.); (M.L.); (S.S.); (M.Z.K.)
| | - Seongjun So
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (Y.L.); (M.L.); (S.S.); (M.Z.K.)
| | - Mustafa Zafer Karagozlu
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (Y.L.); (M.L.); (S.S.); (M.Z.K.)
| | - Go Hun Seo
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.K.); (G.H.S.); (I.H.C.)
| | - In Hee Choi
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.K.); (G.H.S.); (I.H.C.)
| | - Peter C. W. Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Chong-Jai Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Eunju Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (Y.L.); (M.L.); (S.S.); (M.Z.K.)
- Correspondence: (E.K.); (B.H.L.); Tel.: +82-2-3010-8547 (E.K.); +82-2-3010-5950 (B.H.L.)
| | - Beom Hee Lee
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (T.K.); (G.H.S.); (I.H.C.)
- Correspondence: (E.K.); (B.H.L.); Tel.: +82-2-3010-8547 (E.K.); +82-2-3010-5950 (B.H.L.)
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Park J, Hun Seo G, Lee Y, Choi Y, Kang M, Do HS, Kim YH, Jin Yu J, Ai-Rhan Kim E, Jung E, Sop Lee B, Suk Baek J, Hee Lee B. High Prevalence of Genetic Alterations in Infantile-Onset Cardiomyopathy. CONGENIT HEART DIS 2021. [DOI: 10.32604/chd.2021.015167] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ahn H, Seo GH, Oh A, Lee Y, Keum C, Heo SH, Kim T, Choi J, Kim GH, Ko TS, Yum MS, Lee BH, Choi IH. Diagnosis of Schaaf-Yang syndrome in Korean children with developmental delay and hypotonia. Medicine (Baltimore) 2020; 99:e23864. [PMID: 33371171 PMCID: PMC7748310 DOI: 10.1097/md.0000000000023864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/20/2020] [Indexed: 11/25/2022] Open
Abstract
Schaaf-Yang syndrome (SYS) is a recently identified disorder caused by a loss-of-function mutation in a maternally imprinted gene, MAGEL2, at 15q11.2q13. Due to its extreme rarity and wide range of clinical severity, clinical suspicion is difficult for a physician. In the current study, its frequency among the Korean pediatric patients with developmental delay (DD) or intellectual disability (ID) was assessed. As the first report of Korean patients with SYS, our study aims to increase the awareness of this condition among the physicians taking care of the pediatric patients with DD/ID and hypotonia.The patients diagnosed with SYS by whole-exome sequencing (WES) among the 460 Korean pediatric patients with DD/ID were included, and their clinical and molecular features were reviewed.Four patients (0.9%) were diagnosed with SYS. Profound DD (4 patients), multiple anomalies including joint contractures and facial dysmorphism (4 patients), generalized hypotonia (3 patients), and severe respiratory difficulty requiring mechanical ventilation (3 patients) were noted in most cases, similar to those in previous reports. Sleep apnea (2 patients), autistic features (2 patients), a high grade of gastroesophageal reflux (1 patient), and seizures (1 patient) were found as well. A total of 3 different truncating MAGEL2 mutations were identified. A previously-reported mutation, to be the most common one, c.1996dupC, was found in 2 patients. The other 2 mutations, c.2217delC and c.3449_3450delTT were novel mutations. As MAGEL2 is maternally imprinted, 2 patients had inherited the MAGEL2 mutation from their respective healthy fathers.SYS is an extremely rare cause of DD/ID. However, hypotonia, joint contractures, profound DD/ID and facial dysmorphism are the suggestive clinical features for SYS. As a maternally imprinted disorder, it should be reminded that SYS may be inherited in form of a mutation from a healthy father.
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Affiliation(s)
- Hyunji Ahn
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
| | | | - Arum Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
| | - Yena Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
| | | | | | | | | | - Gu-Hwan Kim
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Tae-Sung Ko
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
| | - Mi-Sun Yum
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine
- ASAN Institute for Life Sciences
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - In Hee Choi
- Medical Genetics Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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Shin JH, Seo GH, Oh SH, Chung WY, Kim HY, Kim YM, Bae MH, Park KH, Kwak MJ. An A627V-activating mutation in the thyroid-stimulating hormone receptor gene in familial nonautoimmune hyperthyroidism. Ann Pediatr Endocrinol Metab 2020; 25:282-286. [PMID: 33401884 PMCID: PMC7788338 DOI: 10.6065/apem.2040076.038] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/12/2020] [Indexed: 11/20/2022] Open
Abstract
Nonautoimmune hyperthyroidism is a very rare cause of congenital hyperthyroidism that is usually caused by an activating mutation in the thyroid-stimulating hormone receptor (TSHR) gene. In this report, we describe a case of nonautoimmune hyperthyroidism in a patient with TSHR mutation. Our patient was the younger of a set of twins born at 36 weeks and 6 days of gestation. The patient was noted to be more irritable than the older twin at 80 days of age, and the mother was taking methimazole for Graves' disease that had been diagnosed 12 years prior. Therefore, a thyroid function test was conducted for the patient. The results revealed subclinical hyperthyroidism, and tests of antithyroglobulin antibody, antithyroid peroxidase antibody, and anti-thyroid-stimulating hormone (TSH) receptor antibody were all negative. During follow-up, at around 4 months of age, free T4 increased to 2.89 ng/dL, and TSH was still low at 0.01 μIU/mL; therefore, 3 mg/day of methimazole was initiated. Whole-exome sequencing showed a heterozygous variant of c.1800C>T (p.Ala627Val) in the TSHR gene. Testing in the family confirmed an identical variant in the patient's mother, leading to diagnosis of familial nonautoimmune hyperthyroidism inherited in an autosomal dominant pattern. This is the second report of A627V confirmed as a germline variant.
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Affiliation(s)
- Jung Hyun Shin
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | | | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Inje University Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Hye Young Kim
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Mi Hye Bae
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Kyung Hee Park
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea
| | - Min Jung Kwak
- Department of Pediatrics, Pusan National University Hospital, Busan, Korea,Address for correspondence: Min Jung Kwak, MD, PhD Department of Pediatrics, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 49241, Korea Tel: +82-51-240-7298 Fax: +82-51-248-6205 E-mail:
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Kim MJ, Yum MS, Seo GH, Lee Y, Jang HN, Ko TS, Lee BH. Clinical Application of Whole Exome Sequencing to Identify Rare but Remediable Neurologic Disorders. J Clin Med 2020; 9:jcm9113724. [PMID: 33233562 PMCID: PMC7699758 DOI: 10.3390/jcm9113724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Background: The aim of this study was to describe the application of whole exome sequencing (WES) in the accurate genetic diagnosis and personalized treatment of extremely rare neurogenetic disorders. Methods: From 2017 to 2019, children with neurodevelopmental symptoms were evaluated using WES in the pediatric neurology clinic and medical genetics center. The clinical presentation, laboratory findings including the genetic results from WES, and diagnosis-based treatment and outcomes of the four patients are discussed. Results: A total of 376 children with neurodevelopmental symptom were evaluated by WES, and four patients (1.1%) were diagnosed with treatable neurologic disorders. Patient 1 (Pt 1) showed global muscle hypotonia, dysmorphic facial features, and multiple anomalies beginning in the perinatal period. Pt 1 was diagnosed with congenital myasthenic syndrome 22 of PREPL deficiency. Pt 2 presented with hypotonia and developmental arrest and was diagnosed with autosomal recessive dopa-responsive dystonia due to TH deficiency. Pt 3, who suffered from intractable epilepsy and progressive cognitive decline, was diagnosed with epileptic encephalopathy 47 with a heterozygous FGF12 mutation. Pt 4 presented with motor delay and episodic ataxia and was diagnosed with episodic ataxia type II (heterozygous CACNA1A mutation). The patients’ major neurologic symptoms were remarkably relieved with pyridostigmine (Pt 1), levodopa (Pt 2), sodium channel blocker (Pt 3), and acetazolamide (Pt 4), and most patients regained developmental milestones in the follow-up period (0.4 to 3 years). Conclusions: The early application of WES helps in the identification of extremely rare genetic diseases, for which effective treatment modalities exist. Ultimately, WES resulted in optimal clinical outcomes of affected patients.
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Affiliation(s)
- Min-Jee Kim
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul 05505, Korea; (M.-J.K.); (H.N.J.); (T.-S.K.)
| | - Mi-Sun Yum
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul 05505, Korea; (M.-J.K.); (H.N.J.); (T.-S.K.)
- Correspondence: ; Tel.: +82-2-3010-3386; Fax: +82-2-3010-3356
| | - Go Hun Seo
- 3billion Inc., Seoul 06193, Korea; (G.H.S.); (B.H.L.)
| | - Yena Lee
- Department of Genetics, Asan Medical Center, Ulsan University College of Medicine, 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul 05505, Korea;
| | - Han Na Jang
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul 05505, Korea; (M.-J.K.); (H.N.J.); (T.-S.K.)
| | - Tae-Sung Ko
- Department of Pediatrics, Asan Medical Center Children’s Hospital, Ulsan University College of Medicine 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul 05505, Korea; (M.-J.K.); (H.N.J.); (T.-S.K.)
| | - Beom Hee Lee
- 3billion Inc., Seoul 06193, Korea; (G.H.S.); (B.H.L.)
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