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Xiang J, Sun X, Song N, Ramaswamy S, Abou Tayoun AN, Peng Z. Comprehensive interpretation of single-nucleotide substitutions in GJB2 reveals the genetic and phenotypic landscape of GJB2-related hearing loss. Hum Genet 2023; 142:33-43. [PMID: 36048236 DOI: 10.1007/s00439-022-02479-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/16/2022] [Indexed: 01/18/2023]
Abstract
Genetic variants in GJB2 are the most frequent cause of congenital and childhood hearing loss worldwide. The purpose of this study was to delineate the genetic and phenotypic landscape of GJB2 SNV variants. All possible single-nucleotide substitution variants of the coding region of GJB2 (N = 2043) were manually curated following the ACMG/AMP hearing loss guidelines. As a result, 60 (2.9%), 177 (8.7%), 1499 (73.4%), 301 (14.7%) and 6 (0.3%) of the variants were classified as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, and benign, respectively. 53% (84/158) of the pathogenic/likely pathogenic missense variants were not present in ClinVar. The second transmembrane domain and the 310 helix were highly enriched for pathogenic missense variants, while the intracellular loops were tolerant to variation. The N-terminal tail and the extracellular loop showed high clustering of variants that are associated with syndromic or dominant non-syndromic hearing loss. In conclusion, our study interpreted all possible single-nucleotide substitution coding variants, characterized novel clinically significant variants in GJB2, and revealed significant genotype-phenotype correlations at this common hearing loss locus. Our work provides a prototype for other genes with similarly high genetic and phenotypic heterogeneity.
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Affiliation(s)
- Jiale Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Nana Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sathishkumar Ramaswamy
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Ahmad N Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates. .,Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Zhiyu Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. .,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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Huang S, Zhao G, Wu J, Li K, Wang Q, Fu Y, Zhang H, Bi Q, Li X, Wang W, Guo C, Zhang D, Wu L, Li X, Xu H, Han M, Wang X, Lei C, Qiu X, Li Y, Li J, Dai P, Yuan Y. Gene4HL: An Integrated Genetic Database for Hearing Loss. Front Genet 2021; 12:773009. [PMID: 34733322 PMCID: PMC8558372 DOI: 10.3389/fgene.2021.773009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Hearing loss (HL) is one of the most common disabilities in the world. In industrialized countries, HL occurs in 1–2/1,000 newborns, and approximately 60% of HL is caused by genetic factors. Next generation sequencing (NGS) has been widely used to identify many candidate genes and variants in patients with HL, but the data are scattered in multitudinous studies. It is a challenge for scientists, clinicians, and biologists to easily obtain and analyze HL genes and variant data from these studies. Thus, we developed a one-stop database of HL-related genes and variants, Gene4HL (http://www.genemed.tech/gene4hl/), making it easy to catalog, search, browse and analyze the genetic data. Gene4HL integrates the detailed genetic and clinical data of 326 HL-related genes from 1,608 published studies, along with 62 popular genetic data sources to provide comprehensive knowledge of candidate genes and variants associated with HL. Additionally, Gene4HL supports the users to analyze their own genetic engineering network data, performs comprehensive annotation, and prioritizes candidate genes and variations using custom parameters. Thus, Gene4HL can help users explain the function of HL genes and the clinical significance of variants by correlating the genotypes and phenotypes in humans.
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Affiliation(s)
- Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Jie Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qiuquan Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Ying Fu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Honglei Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Qingling Bi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaohong Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Weiqian Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chang Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Dejun Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xiaoge Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Huiyan Xu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Mingyu Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Wang
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Chen Lei
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Xiaofang Qiu
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Yang Li
- Angen Gene Medicine Technology Co., Ltd., Beijing, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, China
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Lin L, Zhang D, Jin Q, Teng Y, Yao X, Zhao T, Xu X, Jin Y. Mutational Analysis of Mitochondrial tRNA Genes in 200 Patients with Type 2 Diabetes Mellitus. Int J Gen Med 2021; 14:5719-5735. [PMID: 34557026 PMCID: PMC8454214 DOI: 10.2147/ijgm.s330973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
Objective Previous studies showed that variants in mitochondrial DNA (mtDNA) are associated with type 2 diabetes mellitus (T2DM). However, the relationships between mitochondrial tRNA (mt-tRNA) variants and T2DM remain poorly understood. Methods In this study, we performed a mutational screening of 22 mt-tRNA genes in a cohort of 200 Han Chinese subjects with T2DM and 200 control subjects through PCR–Sanger sequencing. The identified mt-tRNA variants were assessed for their pathogenicity via the phylogenetic approach, structural and functional analysis. Furthermore, two Han Chinese pedigrees with maternally inherited diabetes and deafness (MIDD) were reported by clinical and genetic assessments. Results A total of 49 genetic variants in mt-tRNA genes were identified; among them, 31 variants (17 pathogenic/likely pathogenic) were absent in controls, located at extremely conserved nucleotides, may have potential structural and functional significance, thereby considered to be T2DM-associated variants. In addition, sequence analysis of entire mitochondrial genomes of the matrilineal relatives from two MIDD pedigrees revealed the occurrence of tRNALeu(UUR) A3243G and T3290C mutations, as well as sets of polymorphisms belonging to mitochondrial haplogroups F2 and D4. However, the lack of any functional variants in connexin 26 gene (GJB2) and tRNA 5-methylaminomethyl-2-thiouridylate (TRMU) suggested that nuclear genes may not play active roles in clinical expression of MIDD in these pedigrees. Conclusion Our data indicated that mt-tRNA variants were associated with T2DM, screening for mt-tRNA pathogenic mutations was recommended for early detection and prevention of mitochondrial diabetes.
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Affiliation(s)
- Liangyan Lin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Dongdong Zhang
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Qingsong Jin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Yaqin Teng
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Xiaoyan Yao
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Tiantian Zhao
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Xinmiao Xu
- Department of Endocrinology, Yantai Yeda Hospital, Yantai, Shandong, People's Republic of China
| | - Yongjun Jin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
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