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Mianesaz H, Ghalamkari S, Salehi M, Behnam M, Hosseinzadeh M, Basiri K, Ghasemi M, Sedghi M, Ansari B. Causative variants linked with limb girdle muscular dystrophy in an Iranian population: 6 novel variants. Mol Genet Genomic Med 2022; 11:e2101. [PMID: 36374152 PMCID: PMC9938754 DOI: 10.1002/mgg3.2101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/03/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Limb-girdle muscular dystrophy (LGMD) is a non-syndromic muscular dystrophy caused by variations in the genes involved in muscle structure, function and repair. The heterogeneity in the severity, progression, age of onset, and causative genes makes next-generation sequencing (NGS) a necessary approach for the proper diagnosis of LGMD. METHODS In this article, 26 Iranian patients with LGMD criteria were diagnosed with disease variants in the genes encoding calpain3, dysferlin, sarcoglycans and Laminin α-2. Patients were referred to the hospital with variable distribution of muscle wasting and progressive weakness in the body. The symptoms along with biochemical and EMG tests were suggestive of LGMD; thus the genomic DNA of patients were investigated by whole-exome sequencing including flanking intronic regions. The target genes were explored for the disease-causing variants. Moreover, the consequence of the amino acid alterations on proteins' secondary structure and function was investigated for a better understanding of the pathogenicity of variants. Variants were sorted based on the genomic region, type and clinical significance. RESULTS In a comprehensive investigation of previous clinical records, 6 variations were determined as novel, including c.1354-2 A > T and c.3169_3172dupCGGC in DYSF, c.568 G > T in SGCD, c.7243 C > T, c.8662_8663 insT and c. 4397G > C in LAMA2. Some of the detected variants were located in functional domains and/or near to the post-translational modification sites, altering or removing highly conserved regions of amino acid sequence.
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Affiliation(s)
- Hamidreza Mianesaz
- Department of Human Genetics, Medical SchoolUniversity of DebrecenDebrecenHungary,Department of Genetics and Molecular BiologyIsfahan University of Medical SciencesIsfahanIran
| | - Safoura Ghalamkari
- Department of Genetics and Molecular BiologyIsfahan University of Medical SciencesIsfahanIran,Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of MedicineUniversity of DebrecenDebrecenHungary
| | - Mansoor Salehi
- Department of Genetics and Molecular BiologyIsfahan University of Medical SciencesIsfahanIran,Cellular, Molecular and Genetics Research CenterIsfahan University of Medical SciencesIsfahanIran
| | - Mahdiyeh Behnam
- Cellular, Molecular and Genetics Research CenterIsfahan University of Medical SciencesIsfahanIran,Student Research CommitteeSemnan University of Medical ScienceSemnanIran
| | - Majid Hosseinzadeh
- Department of Genetics and Molecular BiologyIsfahan University of Medical SciencesIsfahanIran,Medical Genetics Laboratory, Alzahra University HospitalIsfahan University of Medical SciencesIsfahanIran
| | - Keivan Basiri
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical ScienceTehranIran,Department of NeurologyIsfahan University of Medical SciencesIsfahanIran
| | - Majid Ghasemi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical ScienceTehranIran,Department of NeurologyIsfahan University of Medical SciencesIsfahanIran
| | - Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University HospitalIsfahan University of Medical SciencesIsfahanIran,Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular‐Cellular Sciences InstituteTehran University of Medical ScienceTehranIran
| | - Behnaz Ansari
- Department of NeurologyIsfahan University of Medical SciencesIsfahanIran,Isfahan Neuroscience Research Center, ALzahra Research InstituteIsfahan University of Medical ScienceIsfahanIran
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Zhong H, Zheng Y, Zhao Z, Lin P, Xi J, Zhu W, Lin J, Lu J, Yu M, Zhang W, Lv H, Yan C, Hu J, Wang Z, Lu J, Zhao C, Yuan Y, Luo S. Molecular landscape of CAPN3 mutations in limb-girdle muscular dystrophy type R1: from a Chinese multicentre analysis to a worldwide perspective. J Med Genet 2020; 58:729-736. [PMID: 32994280 DOI: 10.1136/jmedgenet-2020-107159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/31/2020] [Accepted: 08/14/2020] [Indexed: 01/29/2023]
Abstract
BACKGROUND Limb-girdle muscular dystrophy type R1 (LGMDR1) can be caused by recessive CAPN3 mutations accounting for the majority of LGMD. To date, no systemic evaluation has been performed to analyse the detrimental and normal mutations on CAPN3 and its hotspots. METHODS CAPN3 variants (n=112) from a total of 124 patients with LGMDR1 recruited in four centres in China were retrospectively analysed. Then external CAPN3 variants (n=2031) from online databases were integrated with our Chinese cohort data to achieve a worldwide perspective on CAPN3 mutations. According to their related phenotypes (LGMDR1 or normal), we analysed consequence, distribution, ethnicity and severity scores of CAPN3 mutations. RESULTS Two hotspot mutations were identified including c.2120A>G in Chinese population and c.550del in Europe. According to the integrated dataset, 521 mutations were classified as LGMDR1-related and converged on exons 1, 10, 5, 22 and 13 of CAPN3. The remaining 1585 variants were classified as normal-population related. The deleterious ratio of LGMDR1-relevant variants to total variants in each population was 0.26 on average with a maximum of 0.35 in Finns and a minimum of 0.21 in South Asians. Severity evaluation showed that Chinese LGMDR1-related variants exhibited a higher risk (Combined Annotation Dependent Depletion score +1.10) than that from database patients (p<0.001). CONCLUSIONS This study confirmed two hotspots and LGMDR1-related CAPN3 variants, highlighting the advantages in using a data-based comprehensive analysis to achieve a genetic landscape for patients with LGMDR1.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhe Zhao
- Department of Neuromuscular Disorders, Hebei Medical University Third Affiliated Hospital, Shijiazhuang, China
| | - Pengfei Lin
- Department of Neurology, Shandong University Qilu Hospital, Jinan, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Jie Lin
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Jun Lu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chuanzhu Yan
- Department of Neurology, Shandong University Qilu Hospital, Jinan, China
| | - Jing Hu
- Department of Neuromuscular Disorders, Hebei Medical University Third Affiliated Hospital, Shijiazhuang, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jiahong Lu
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Sushan Luo
- Department of Neurology, Huashan Hospital Fudan University, Shanghai, China
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Mojbafan M, Nojehdeh ST, Rahiminejad F, Nilipour Y, Tonekaboni SH, Zeinali S. Reporting a rare form of myopathy, myopathy with extrapyramidal signs, in an Iranian family using next generation sequencing: a case report. BMC MEDICAL GENETICS 2020; 21:77. [PMID: 32293312 PMCID: PMC7158096 DOI: 10.1186/s12881-020-01016-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Abstract
Background Myopathy with extrapyramidal signs (MPXPS) is an autosomal recessive mitochondrial disorder which is caused by mutation in mitochondrial calcium uptake 1 (MICU1) gene located on chromosome 10q22.1. Next Generation Sequencing (NGS) technology is the most effective method for identification of pathogenic variants with the ability to overcome some limitations which Sanger sequencing may encountered. There are few reports on this rare disease around the world and here in this study we first revealed genetic identification of two affected individuals in an Iranian family with a novel mutation. Case presentation The proband was a 5-year-old girl from consanguenous parents. She was first clinically suspicious of affected with limb-girdle muscular dystrophy (LGMD). Muscle biopsy studies and autozygosity mapping, using four short tandem repeat (STR) markers linked to 6 genes of the most prevalent forms of LGMD, ruled out calpainopathy, dysferlinopathy, and sarcoglycanopathis. DNA sample of the proband was sent for NGS. Whole exome sequencing (WES) revealed a novel mutation c.1295delA in exon 13 of MICU1 gene. This homozygous deletion creates a frameshift and a premature stop codon downstream of canonical EF4 calcium binding motif of MICU1. According to the American College of Medical Genetics and Genomics (ACMG) guidline for sequence interpretation, this variant was a pathogenic one. Sanger sequencing in all family members confirmed the results of the WES. Conclusions This study was the first report of MPXPS in Iranian population which also revealed a novel mutation in the MICU1 gene.
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Affiliation(s)
- Marzieh Mojbafan
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Shahid Hemmat Highway, Tehran, Iran.,Department of medical genetics, Ali-Asghar Children's Hospital, Zafar St., Shahid Modarres Highway, Tehran, Iran
| | - Somayeh Takrim Nojehdeh
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41, Majlesi St., Valieasr Ave, Tehran, Iran
| | - Faezeh Rahiminejad
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41, Majlesi St., Valieasr Ave, Tehran, Iran
| | - Yalda Nilipour
- Pathology Department, Pediatric Pathology Research Center, Research Institute for Children Health, Mofid Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Hasan Tonekaboni
- Pediatric Neurology Center of Excellence, Department of Pediatric Neurology, Mofid Children Hospital, Faculty of Medicine, Shahid Beheshti Medical University, Tehran, Iran
| | - Sirous Zeinali
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41, Majlesi St., Valieasr Ave, Tehran, Iran. .,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, No. 69, Pasteur Ave, Tehran, Iran.
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