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Sakuma N, Nishio SY, Goto SI, Honkura Y, Oda K, Takeda H, Kobayashi M, Kumakawa K, Iwasaki S, Takahashi M, Ito T, Arai Y, Isono Y, Obara N, Matsunobu T, Okubo K, Usami SI. Detailed Clinical Features of PTPRQ-Associated Hearing Loss Identified in a Large Japanese Hearing Loss Cohort. Genes (Basel) 2024; 15:489. [PMID: 38674423 PMCID: PMC11050587 DOI: 10.3390/genes15040489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The PTPRQ gene has been identified as one of the genes responsible for non-syndromic sensorineural hearing loss (SNHL), and assigned as DFNA73 and DFNB84. To date, about 30 causative PTPRQ variants have been reported to cause SNHL. However, the detailed clinical features of PTPRQ-associated hearing loss (HL) remain unclear. In this study, 15,684 patients with SNHL were enrolled and genetic analysis was performed using massively parallel DNA sequencing (MPS) for 63 target deafness genes. We identified 17 possibly disease-causing PTPRQ variants in 13 Japanese patients, with 15 of the 17 variants regarded as novel. The majority of variants identified in this study were loss of function. Patients with PTPRQ-associated HL mostly showed congenital or childhood onset. Their hearing levels at high frequency deteriorated earlier than that at low frequency. The severity of HL progressed from moderate to severe or profound HL. Five patients with profound or severe HL received cochlear implantation, and the postoperative sound field threshold levels and discrimination scores were favorable. These findings will contribute to a greater understanding of the clinical features of PTPRQ-associated HL and may be relevant in clinical practice.
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Affiliation(s)
- Naoko Sakuma
- Department of Otorhinolaryngology, Head and Neck Surgery, Nippon Medical School, Tokyo 113-8603, Japan; (N.S.); (T.M.); (K.O.)
| | - Shin-ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1, Asahi, Matsumoto City 390-8621, Japan;
| | - Shin-ichi Goto
- Department of Otorhinolaryngology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8560, Japan;
| | - Yohei Honkura
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University School of Medicine, Sendai 980-8575, Japan;
| | - Kiyoshi Oda
- Department of Otolaryngology, Tohoku Rosai Hospital, Sendai 981-8563, Japan;
| | - Hidehiko Takeda
- Department of Otorhinolaryngology, Toranomon Hospital, Tokyo 105-8470, Japan; (H.T.); (M.K.)
| | - Marina Kobayashi
- Department of Otorhinolaryngology, Toranomon Hospital, Tokyo 105-8470, Japan; (H.T.); (M.K.)
| | - Kozo Kumakawa
- Department of Otolaryngology, Kamio Memorial Hospital, Tokyo 101-0063, Japan;
- Akasaka Toranomon Clinic, Tokyo 107-0052, Japan
| | - Satoshi Iwasaki
- Department of Otorhinolaryngology, International University of Health and Welfare, Mita Hospital, Tokyo 108-8329, Japan; (S.I.); (M.T.)
| | - Masahiro Takahashi
- Department of Otorhinolaryngology, International University of Health and Welfare, Mita Hospital, Tokyo 108-8329, Japan; (S.I.); (M.T.)
| | - Taku Ito
- Department of Otorhinolaryngology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
| | - Yasuhiro Arai
- Department of Otorhinolaryngology-Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama 236-0004, Japan;
| | - Yasuhiro Isono
- Department of Otolaryngology, Yokohama City University Medical Center, Yokohama 232-0024, Japan;
| | - Natsuko Obara
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu City 501-1194, Japan;
| | - Takeshi Matsunobu
- Department of Otorhinolaryngology, Head and Neck Surgery, Nippon Medical School, Tokyo 113-8603, Japan; (N.S.); (T.M.); (K.O.)
| | - Kimihiro Okubo
- Department of Otorhinolaryngology, Head and Neck Surgery, Nippon Medical School, Tokyo 113-8603, Japan; (N.S.); (T.M.); (K.O.)
| | - Shin-ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1, Asahi, Matsumoto City 390-8621, Japan;
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Ford CL, Riggs WJ, Quigley T, Keifer OP, Whitton JP, Valayannopoulos V. The natural history, clinical outcomes, and genotype-phenotype relationship of otoferlin-related hearing loss: a systematic, quantitative literature review. Hum Genet 2023; 142:1429-1449. [PMID: 37679651 PMCID: PMC10511631 DOI: 10.1007/s00439-023-02595-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023]
Abstract
Congenital hearing loss affects one in 500 newborns. Sequence variations in OTOF, which encodes the calcium-binding protein otoferlin, are responsible for 1-8% of congenital, nonsyndromic hearing loss and are the leading cause of auditory neuropathy spectrum disorders. The natural history of otoferlin-related hearing loss, the relationship between OTOF genotype and hearing loss phenotype, and the outcomes of clinical practices in patients with this genetic disorder are incompletely understood because most analyses have reported on small numbers of cases with homogeneous OTOF genotypes. Here, we present the first systematic, quantitative literature review of otoferlin-related hearing loss, which analyzes patient-specific data from 422 individuals across 61 publications. While most patients display a typical phenotype of severe-to-profound hearing loss with prelingual onset, 10-15% of patients display atypical phenotypes, including mild-to-moderate, progressive, and temperature-sensitive hearing loss. Patients' phenotypic presentations appear to depend on their specific genotypes. For example, non-truncating variants located in and immediately downstream of the C2E calcium-binding domain are more likely to produce atypical phenotypes. Additionally, the prevalence of certain sequence variants and their associated phenotypes varies between populations due to evolutionary founder effects. Our analyses also suggest otoacoustic emissions are less common in older patients and those with two truncating OTOF variants. Critically, our review has implications for the application and limitations of clinical practices, including newborn hearing screenings, hearing aid trials, cochlear implants, and upcoming gene therapy clinical trials. We conclude by discussing the limitations of available research and recommendations for future studies on this genetic cause of hearing loss.
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Li X, Shi L, Wang L. A review of the mechanisms underlying the role of the GIPC3 gene in hereditary deafness. Front Synaptic Neurosci 2023; 14:1101587. [PMID: 36704659 PMCID: PMC9872657 DOI: 10.3389/fnsyn.2022.1101587] [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: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
The GAIP interacting protein c terminus (GIPC) genes encode a small family of proteins characterized by centrally located PDZ domains. GIPC3 encodes a 312 amino acid protein. Variants of human GIPC3 are associated with non-syndromic hearing loss. GIPC3 is one of over a hundred different genes with variants causing human deafness. Screening for variants of GIPC3 is essential for early detection of hearing loss in children and eventually treatment of deafness. Accordingly, this paper assesses the status of research developments on the role of GIPC3 in hereditary deafness and the effects of pathogenic variants on the auditory system.
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Affiliation(s)
- Xinxin Li
- Department of Otolaryngology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lin Shi
- Department of Otolaryngology, First Affiliated Hospital of Dalian Medical University, Dalian, China,*Correspondence: Lin Shi,
| | - Liang Wang
- National Joint Engineering Laboratory, Stem Cell Clinical Research Center, Regenerative Medicine Center, First Affiliated Hospital of Dalian Medical University, Dalian, China,Liang Wang,
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Jin Y, Liu XZ, Xie L, Xie W, Chen S, Sun Y. Targeted Next-Generation Sequencing Identified Novel Compound Heterozygous Variants in the PTPRQ Gene Causing Autosomal Recessive Hearing Loss in a Chinese Family. Front Genet 2022; 13:884522. [PMID: 35899188 PMCID: PMC9310072 DOI: 10.3389/fgene.2022.884522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Hearing loss is among the most common congenital sensory impairments. Genetic causes account for more than 50% of the cases of congenital hearing loss. The PTPRQ gene, encoding protein tyrosine phosphatase receptor Q, plays an important role in maintaining the stereocilia structure and function of hair cells. Mutations in the PTPRQ gene have been reported to cause hereditary sensorineural hearing loss. By using next-generation sequencing and Sanger sequencing, we identified a novel compound heterozygous mutation (c.997 G > A and c.6603-3 T > G) of the PTPRQ gene in a Chinese consanguineous family. This is the first report linking these two mutations to recessive hereditary sensorineural hearing loss. These findings contribute to the understanding of the relationship between genotype and hearing phenotype of PTPRQ-related hearing loss, which may be helpful to clinical management and genetic counseling.
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Affiliation(s)
- Yuan Jin
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Zhou Liu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Le Xie
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen Xie
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sen Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Tongji Medical College, Institute of Otorhinolaryngology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yu Sun,
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Genetic profiles of non-syndromic severe-profound hearing loss in Chinese Hans by whole-exome sequencing. Gene 2022; 819:146258. [PMID: 35114279 DOI: 10.1016/j.gene.2022.146258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 11/20/2022]
Abstract
Hereditary hearing loss is highly heterogeneous. Despite over 120 non-syndromic deafness genes have been identified, there are still some of novel genes and variants being explored. In the study, we investigated 105 Chinese Han children with non-syndromic, prelingual, severe-profound hearing loss by whole-exome sequencing on DNA samples. The most common deafness gene was GJB2, mainly in variant c.235delC (p.Leu79CysfsTer3). 14 children were identified with pathogenic mutations in three genes, GJB2, SLC26A4, and OTOF. Two mutations have been identified to be pathogenic and not recorded previously, including c.4691G > A (p.Trp1564Ter) and c.3928_3930dup (p.Lys1310dup) in OTOF. The rare variants c.1349G > A (p.Arg450His) and c.456 T > G (p.Asn152Lys) in GSDME, and c.1595G > T (p.Ser532Ile) in SLC26A4 were detected. The frequency of nonsense variant c.2359G > T (p.Glu787Ter) in OTOA was very high in 17 cases. Four of them were identified to be digenic inheritance, including GJB2 and COL4A4, GJB2 and EYA1, GJB2 and COL4A5, and GJB2 and DFNA5. The findings showed that a novel pathogenic variant and rare variants may be associated with severe and profound hearing loss.
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Fu Y, Huang S, Gao X, Han M, Wang G, Kang D, Yuan Y, Dai P. Analysis of the genotype–phenotype correlation of MYO15A variants in Chinese non-syndromic hearing loss patients. BMC Med Genomics 2022; 15:71. [PMID: 35346193 PMCID: PMC8962197 DOI: 10.1186/s12920-022-01201-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Mutations in the MYO15A gene are a widely recognized cause of autosomal recessive non-syndromic sensorineural hearing loss (NSHL) globally. Here, we examined the role and the genotype–phenotype correlation of MYO15A variants in a cohort of Chinese NSHL cases.
Methods
Eighty-one cases with evidenced MYO15A variants from the 2263 Chinese NSHL cases, who underwent next-generation sequencing (NGS), were enrolled in the study. We investigated the association of MYO15A variants with the severity, progression and age of onset of hearing loss, as well as compared it to the previous reports in different nationalities. The cases were divided into groups according to the number of truncating variants: 2 truncating, 1 truncating and 1 non-truncating, 2 non-truncating variants, and compared the severity of HL among the groups.
Results
MYO15A accounted for 3.58% (81/2263) of all NSHL cases. We analyzed 81 MYO15A-related NSHL cases, 73 of whom were with congenital bilateral, symmetric or severe-to-profound hearing loss (HL), however, 2 of them had a postlingual, asymmetric, mild or moderate HL. There were 102 variants identified in all MYO15A structural domains, 76.47% (78/102) of whom were novel. The most common types of detected variants were missense (44/102, 43.14%), followed by frameshift (27/102, 26.47%), nonsense (14/102, 13.72%), splice site (10/102, 9.80%), in frame (4/102, 3.92%), non-coding (2/102, 1.96%) and synonymous (1/102, 0.98%). The most recurrent variant c.10245_10247delCTC was detected in 12 cases. We observed that the MYO15A variants, located in its N-terminal, motor and FERM domains, led to partial deafness with better residual hearing at low frequencies. There were 34 cases with biallelic truncating variants, 37 cases with monoallelic truncating variants, and 13 cases with biallelic non-truncating variants. The biallelic non-truncating variants group had the least number of cases (12/81), and most of them (10/12) were with profound NSHL.
Conclusions
MYO15A is a major gene responsible for NSHL in China. Cases with MYO15A variants mostly showed early-onset, symmetric, severe-to-profound hearing loss. This study is by far the largest focused on the evaluation of the genotype–phenotype correlations among the variants in the MYO15A gene and its implication in the outcome of NSHL. The biallelic non-truncating MYO15A variants commonly caused profound HL, and the cases with one or two truncating MYO15A variants tended to increase the risk of HL. Nevertheless, further investigations are needed to clarify the causes for the variable severities and progression rates of hearing loss and the detected MYO15A variants in these cases.
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Souissi A, Gibriel AA, Masmoudi S. Genetics and meta-analysis of recessive non-syndromic hearing impairment and Usher syndrome in Maghreb population: lessons from the past, contemporary actualities and future challenges. Hum Genet 2021; 141:583-593. [PMID: 34268600 DOI: 10.1007/s00439-021-02314-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Hereditary hearing impairment (HI) is a heterogeneous condition with over 130 genes associated with genetic non-syndromic HI (NSHI) and Usher syndrome (USH). Approximately 80% of hereditary NSHI cases have autosomal recessive (AR) mode of inheritance. The high rate of consanguinity and endogamy in the Maghreb countries, including Tunisia, Algeria and Morocco, represents a major contributing factor to the development of ARHI. Since the 90s, those populations, with their particular large familiar structure, represented an effective key towards the discovery of the first HI loci and genes. In this study, we performed a deep literature database search to analyze the mutational spectrum and the distribution of pathogenic variants responsible of USH and the NSHI among those populations. To date, 124 pathogenic variants were identified in 32 genes of which over 70% represent population-specific variants. The particular variants' distribution is related to the high rate of consanguinity as well as the multiple shared features such as demographic history of migrations and social behavior that promoted the spreading of several founder mutations within those countries. This is the first study to report lessons from the past and current actualities of HI within the three Maghreb countries. However, despite the great impact placed by such population for the HI genetic studies, only a few next-generation sequencing platforms have so far been implemented with those countries. We, therefore, believe that those countries should be supported to implement this technology that would definitely be of great value in the discovery of additional novel HI genes/variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia
| | - Abdullah A Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia.
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Moussaoui A, El Qabli M, Adarmouch L, Aboussair N. The frequency of the homozygote 35delG mutation in the connexin 26 gene in North African with non-syndromic hearing loss: A meta-analysis study. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Petrova NV, Marakhonov AV, Balinova NV, Abrukova AV, Konovalov FA, Kutsev SI, Zinchenko RA. Genetic Variant c.245A>G (p.Asn82Ser) in GIPC3 Gene Is a Frequent Cause of Hereditary Nonsyndromic Sensorineural Hearing Loss in Chuvash Population. Genes (Basel) 2021; 12:820. [PMID: 34071867 PMCID: PMC8226456 DOI: 10.3390/genes12060820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 11/05/2022] Open
Abstract
Hereditary nonsyndromic sensorineural hearing loss is a disease in which hearing loss occurs due to damage to the organ of the inner ear, the auditory nerve, or the center in the brain that is responsible for the perception of sound, characterized by wide locus and allelic heterogeneity and different types of inheritance. Given the diversity of population of the Russian Federation, it seems necessary to study the ethnic characteristics of the molecular causes of the disease. The aim is to study the molecular and genetic causes of hereditary sensorineural hearing loss in Chuvash, the fifth largest ethnic group in Russia. DNA samples of 26 patients from 21 unrelated Chuvash families from the Republic of Chuvashia, in whom the diagnosis of hereditary sensorineural hearing loss had been established, were analyzed using a combination of targeted Sanger sequencing, multiplex ligase-dependent probe amplification, and whole exome sequencing. The homozygous variant NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) is the major molecular cause of hereditary sensorineural hearing loss in 23% of Chuvash patients (OMIM #601869). Its frequency was 25% in patients and 1.1% in healthy Chuvash population. Genotyping of the NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) variant in five neighboring populations from the Volga-Ural region (Russian, Udmurt, Mary, Tatar, Bushkir) found no evidence that this variant is common in those populations.
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Affiliation(s)
- Nika V. Petrova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Natalia V. Balinova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Anna V. Abrukova
- Presidential Perinatal Center of the Public Health Ministry of Chuvashia, Genetic Counseling Department, 428018 Cheboksary, Russia;
| | | | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (N.V.P.); (N.V.B.); (S.I.K.); (R.A.Z.)
- N.A. Semashko National Research Institute of Public Health, 105064 Moscow, Russia
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Souissi A, Ben Said M, Ben Ayed I, Elloumi I, Bouzid A, Mosrati MA, Hasnaoui M, Belcadhi M, Idriss N, Kamoun H, Gharbi N, Gibriel AA, Tlili A, Masmoudi S. Novel pathogenic mutations and further evidence for clinical relevance of genes and variants causing hearing impairment in Tunisian population. J Adv Res 2021; 31:13-24. [PMID: 34194829 PMCID: PMC8240103 DOI: 10.1016/j.jare.2021.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Hearing impairment (HI) is characterized by complex genetic heterogeneity. The evolution of next generation sequencing, including targeted enrichment panels, has revolutionized HI diagnosis. Objectives In this study, we investigated genetic causes in 22 individuals with non-GJB2 HI. Methods We customized a HaloplexHS kit to include 30 genes known to be associated with autosomal recessive nonsyndromic HI (ARNSHI) and Usher syndrome in North Africa. Results In accordance with the ACMG/AMP guidelines, we report 11 pathogenic variants; as follows; five novel variants including three missense (ESRRB-Tyr295Cys, MYO15A-Phe2089Leu and MYO7A-Tyr560Cys) and two nonsense (USH1C-Gln122Ter and CIB2-Arg104Ter) mutations; two previously reported mutations (OTOF-Glu57Ter and PNPT1-Glu475Gly), but first time identified among Tunisian families; and four other identified mutations namely WHRN-Gly808AspfsX11, SLC22A4-Cys113Tyr and two MYO7A compound heterozygous splice site variants that were previously described in Tunisia. Pathogenic variants in WHRN and CIB2 genes, in patients with convincing phenotype ruling out retinitis pigmentosa, provide strong evidence supporting their association with ARNSHI. Moreover, we shed lights on the pathogenic implication of mutations in PNPT1 gene in auditory function providing new evidence for its association with ARNSHI. Lack of segregation of a previously identified causal mutation OTOA-Val603Phe further supports its classification as variant of unknown significance. Our study reports absence of otoacoustic emission in subjects using bilateral hearing aids for several years indicating the importance of screening genetic alteration in OTOF gene for proper management of those patients. Conclusion In conclusion, our findings do not only expand the spectrum of HI mutations in Tunisian patients, but also improve our knowledge about clinical relevance of HI causing genes and variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mohamed Ali Mosrati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Malek Belcadhi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Nourhene Gharbi
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Abdullah A. Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy. The British University in Egypt (BUE) Cairo, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
- Corresponding author at: Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sidi Mansour road Km 6, BP “1177”, 3018 Sfax, Tunisia.
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11
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Noman M, Bukhari SA, Rehman S, Qasim M, Ali M, Riazuddin S, Ahmed ZM. Identification and computational analysis of USH1C, and SLC26A4 variants in Pakistani families with prelingual hearing loss. Mol Biol Rep 2020; 47:9987-9993. [PMID: 33231815 PMCID: PMC10680121 DOI: 10.1007/s11033-020-06016-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/16/2020] [Indexed: 12/16/2022]
Abstract
Hearing loss (HL) is clinically and genetically heterogeneous disorder and is the most frequent occurring sensory deficit in humans. This study was conducted to decipher the genetic cause of HL occurring in two large consanguineous Pakistani families (GCNF-01, GCNF-03). Family history and pure tone audiometry of both families suggested prelingual HL, while the affected individuals of GCNF-01 also had low vision and balance problems, consistent with cardinal features of Usher syndrome type I (USH1). Exome sequencing followed by segregating analysis revealed a novel splice site variant (c.877-1G > A) of USH1C occurring with USH1 phenotype in family GCNF01. While the affected individual of family GCNF-03 were homozygous for the c.716 T > A, p.(Val239Asp) previously reported pathogenic variant of SLC26A4. Both variants have very low frequencies in control database. In silico mutagenesis and 3-dimensional simulation analyses revealed that both variants have deleterious impact on the proteins folding and secondary structures. Our study expands the mutation spectrum of the HL genes and emphasizes the utility of exome sequencing coupled with bioinformatics tools for clinical genetic diagnosis, prognosis, and family counseling.
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Affiliation(s)
- Muhammad Noman
- Department of Biochemistry, Government College University, Faisalabad, 38000, Pakistan
| | - Shazia A Bukhari
- Department of Biochemistry, Government College University, Faisalabad, 38000, Pakistan.
| | - Sakina Rehman
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Muhammad Qasim
- Department of Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Muhammad Ali
- Department of Animal Sciences, Quaid Azam University, Islamabad, 46000, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
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12
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KALAIMATHI MURUGESAN, SUBATHRA MAHALINGAM, JEFFREY JUSTINMARGRET, SELVAKUMARI MATHIYALAGAN, CHANDRU JAYASANKARAN, SHARANYA NARASIMHAN, PARIDHY VANNIYAS, SRISAILAPATHY CRSRIKUMARI. Low incidence of GIPC3 variants among the prelingual hearing impaired from southern India. J Genet 2020. [DOI: 10.1007/s12041-020-01234-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Novel Mutations in CLPP, LARS2, CDH23, and COL4A5 Identified in Familial Cases of Prelingual Hearing Loss. Genes (Basel) 2020; 11:genes11090978. [PMID: 32842620 PMCID: PMC7564084 DOI: 10.3390/genes11090978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
We report the underlying genetic causes of prelingual hearing loss (HL) segregating in eight large consanguineous families, ascertained from the Punjab province of Pakistan. Exome sequencing followed by segregation analysis revealed seven potentially pathogenic variants, including four novel alleles c.257G>A, c.6083A>C, c.89A>G, and c.1249A>G of CLPP, CDH23, COL4A5, and LARS2, respectively. We also identified three previously reported HL-causing variants (c.4528C>T, c.35delG, and c.1219T>C) of MYO15A, GJB2, and TMPRSS3 segregating in four families. All identified variants were either absent or had very low frequencies in the control databases. Our in silico analyses and 3-dimensional (3D) molecular modeling support the deleterious impact of these variants on the encoded proteins. Variants identified in MYO15A, GJB2, TMPRSS3, and CDH23 were classified as “pathogenic” or “likely pathogenic”, while the variants in CLPP and LARS2 fall in the category of “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. This paper highlights the genetic diversity of hearing disorders in the Pakistani population and reports the identification of four novel mutations in four HL families.
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14
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Whole exome sequencing identifies novel compound heterozygous pathogenic variants in the MYO15A gene leading to autosomal recessive non-syndromic hearing loss. Mol Biol Rep 2020; 47:5355-5364. [DOI: 10.1007/s11033-020-05618-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
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15
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Budde BS, Aly MA, Mohamed MR, Breß A, Altmüller J, Motameny S, Kawalia A, Thiele H, Konrad K, Becker C, Toliat MR, Nürnberg G, Sayed EAF, Mohamed ES, Pfister M, Nürnberg P. Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss. Clin Genet 2020; 98:32-42. [DOI: 10.1111/cge.13754] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Birgit S. Budde
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Maha Abdelgaber Aly
- Cologne Center for Genomics University of Cologne Cologne Germany
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Mostafa R. Mohamed
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Andreas Breß
- Department of Otolaryngology University of Tübingen Tübingen Germany
| | - Janine Altmüller
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Susanne Motameny
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Amit Kawalia
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Holger Thiele
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Kathryn Konrad
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Christian Becker
- Cologne Center for Genomics University of Cologne Cologne Germany
| | | | - Gudrun Nürnberg
- Cologne Center for Genomics University of Cologne Cologne Germany
| | | | - Enass Sayed Mohamed
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Markus Pfister
- Department of Otolaryngology University of Tübingen Tübingen Germany
- HNO Sarnen GmbH & Swisstinnitus AG Sarnen Switzerland
| | - Peter Nürnberg
- Cologne Center for Genomics University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne University of Cologne Cologne Germany
- ATLAS Biolabs GmbH Berlin Germany
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16
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Koohiyan M. A systematic review of SLC26A4 mutations causing hearing loss in the Iranian population. Int J Pediatr Otorhinolaryngol 2019; 125:1-5. [PMID: 31228605 DOI: 10.1016/j.ijporl.2019.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/19/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. In spite of this, mutations in the SLC26A4 gene, have been reported to be the second most common contributor after those of GJB2 in many populations. However, different results have been reported for the frequency of SLC26A4 mutations in Iran, which varies between 0 and 12.3%. Here, we have taken together and reviewed the spectrum and frequency of the reported SLC26A4 mutations to provide a comprehensive collection of data for SLC26A4 mutations and HL in the Iranian population and considered founder mutations. METHODS A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases was conducted for articles published before March 2019. The primary data of these studies including the number of samples, mutation frequency and so on were extracted. RESULTS Nine studies involved 827 unrelated families were included and analyzed for the type and prevalence of the SLC26A4 gene mutations. Altogether 39 different genetic mutations were detected. SLC26A4 mutations were found to be 6.39% in the population studied which is significantly lower than that identified in the east Asia. However, c.1334T > G was the most common mutation accounting for 10% of the populations studied. CONCLUSIONS This data gives an overview of the SLC26A4 mutations in Iran, which could be used for screening, diagnostic programs of live births and genetic counseling.
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Affiliation(s)
- Mahbobeh Koohiyan
- Cancer Research Center, Shahrekord University of Medical Sciences, Rahmatieh, Shahrekord, 8813833435, Iran.
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17
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Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss. Genes (Basel) 2019; 10:genes10090715. [PMID: 31527525 PMCID: PMC6770988 DOI: 10.3390/genes10090715] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/03/2022] Open
Abstract
The OTOA gene (Locus: DFNB22) is reported to be one of the causative genes for non-syndromic autosomal recessive hearing loss. The copy number variations (CNVs) identified in this gene are also known to cause hearing loss, but have not been identified in Japanese patients with hearing loss. Furthermore, the clinical features of OTOA-associated hearing loss have not yet been clarified. In this study, we performed CNV analyses of a large Japanese hearing loss cohort, and identified CNVs in 234 of 2262 (10.3%, 234/2262) patients with autosomal recessive hearing loss. Among the identified CNVs, OTOA gene-related CNVs were the second most frequent (0.6%, 14/2262). Among the 14 cases, 2 individuals carried OTOA homozygous deletions, 4 carried heterozygous deletions with single nucleotide variants (SNVs) in another allele. Additionally, 1 individual with homozygous SNVs in the OTOA gene was also identified. Finally, we identified 7 probands with OTOA-associated hearing loss, so that its prevalence in Japanese patients with autosomal recessive hearing loss was calculated to be 0.3% (7/2262). As novel clinical features identified in this study, the audiometric configurations of patients with OTOA-associated hearing loss were found to be mid-frequency. This is the first study focused on the detailed clinical features of hearing loss caused by this gene mutation and/or gene deletion.
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Talbi S, Bonnet C, Boudjenah F, Mansouri MT, Petit C, Ammar Khodja F. The spectrum of GJB2 gene mutations in Algerian families with nonsyndromic hearing loss from Sahara and Kabylie regions. Int J Pediatr Otorhinolaryngol 2019; 124:157-160. [PMID: 31200317 DOI: 10.1016/j.ijporl.2019.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023]
Abstract
INTRODUCTION DFNB1, caused by mutations of GJB2 or GJB6, is the most prevalent genetic form of nonsyndromic (i.e., isolated) congenital deafness in countries located around the Mediterranean Sea. Because some mutations are restricted to specific ethnic-geographic groups, we studied the prevalence and spectrum of GJB2/GJB6 mutations in deaf patients originating from two different Algerian regions, Kabylie and Sahara. PATIENTS AND METHODS Among 91 reportedly unrelated Algerian patients affected by prelingual deafness, 80 patients (41 from Kabylie and 39 from Sahara) were diagnosed with isolated deafness. All had profound deafness, except one patient with mild deafness. They were screened for the presence of GJB2 mutations by direct sequencing of the single coding exon of GJB2. Patients without mutations were then screened for the presence of the most frequent two deletions of GJB6: del(GJB6-D13S1854) and del(GJB6-D13S1830). RESULTS Causative mutations were found in 13 and 8 patients from Kabylie and Sahara, respectively, accounting for more than a quarter of the cohort. The c.35delG, p.Gly12Valfs*2 mutation remains the most important mutation both in Kabylie (10 patients) and Sahara (7 patients). All detected patients were homozygous for this mutation. In addition, two other mutations (c.139G > T, p.Glu47* and c.167delT, p.Leu56Argfs*26) were found homozygous in one family each, and two patients were compound heterozygotes for (c.35delG p.Gly12Valfs*2/c.139G > T, p.Glu47*). No deletion of GJB6 was detected. CONCLUSION We confirm that mutations in GJB2, mainly c.35delG, are one of the most prevalent causes of nonsyndromic congenital deafness in Algeria, whereas the del (GJB6-D13S1854) and del (GJB6-D13S1830) deletions of GJB6 contribute little, if any. Further investigation is needed to identify the cause of deafness in other patients without diagnostic.
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Affiliation(s)
- Sonia Talbi
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene (USTHB), POB32 ElAlia, 16111, Bab Ezzouar, Alger, Algeria.
| | - Crystel Bonnet
- Inserm UMRS 1120, Institut de la Vision, Sorbonne Université, Paris, France
| | - Farid Boudjenah
- Service d'Otorhinolaryngologie (ORL), Hôpital de Frantz fanon, Bejaia, Algeria; Service d'Otorhinolaryngologie (ORL), Hôpital Sidi Belloua, Tizi-Ouzou, Algeria
| | | | - Christine Petit
- Inserm UMRS 1120, Institut de la Vision, Sorbonne Université, Paris, France; Institut Pasteur, Collège de France, Paris, France
| | - Fatima Ammar Khodja
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene (USTHB), POB32 ElAlia, 16111, Bab Ezzouar, Alger, Algeria
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19
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Zhang J, Guan J, Wang H, Yin L, Wang D, Zhao L, Zhou H, Wang Q. Genotype-phenotype correlation analysis of MYO15A variants in autosomal recessive non-syndromic hearing loss. BMC MEDICAL GENETICS 2019; 20:60. [PMID: 30953472 PMCID: PMC6451310 DOI: 10.1186/s12881-019-0790-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/20/2019] [Indexed: 12/13/2022]
Abstract
Background MYO15A variants are responsible for human non-syndromic autosomal recessive deafness (DFNB3). The majority of MYO15A variants are associated with a congenital severe-to-profound hearing loss phenotype, except for MYO15A variants in exon 2, which cause a milder auditory phenotype, suggesting a genotype-phenotype correlation of MYO15A. However, MYO15A variants not in exon 2 related to a milder phenotype have also been reported, indicating that the genotype-phenotype correlation of MYO15A is complicated. This study aimed to provide more cases of MYO15A variation with diverse phenotypes to analyse this complex correlation. Methods Fifteen Chinese autosomal recessive non-syndromic hearing loss (ARNSHL) individuals with MYO15A variants (8 males and 7 females) from 14 unrelated families, identified by targeted gene capture of 127 known candidate deafness genes, were recruited. Additionally, we conducted a review of the literature to further analyses all reported MYO15A genotype-phenotype relationships worldwide. Results We identified 16 novel variants and 12 reported pathogenic MYO15A variants in 15 patients, two of which presented with a milder phenotype. Interestingly, one of these cases carried two reported pathogenic variants in exon 2, while the other carried two novel variants not in exon 2. Based on our literature review, MYO15A genotype-phenotype correlation analysis showed that almost all domains were reported to be correlated with a milder phenotype. However, variants in the N-terminal domain were more likely to cause a milder phenotype. Using next-generation sequencing (NGS), we also found that the number of known MYO15A variants with milder phenotypes in Southeast Asia has increased in recent years. Conclusion Our work extended the MYO15A variant spectrum, enriched our knowledge of auditory phenotypes, and tried to explore the genotype-phenotype correlation in different populations in order to investigate the cause of the complex MYO15A genotype-phenotype correlation. Electronic supplementary material The online version of this article (10.1186/s12881-019-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Zhang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.,Department of Otolaryngology of Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Jing Guan
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.
| | - Hongyang Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | | | - Dayong Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | - Lidong Zhao
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China
| | - Huifang Zhou
- Department of Otolaryngology of Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Qiuju Wang
- Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, China.
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20
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Kim BJ, Kim DK, Han JH, Oh J, Kim AR, Lee C, Kim NK, Park HR, Kim MY, Lee S, Lee S, Oh DY, Park WY, Park S, Choi BY. Clarification of glycosylphosphatidylinositol anchorage of OTOANCORIN and human OTOA variants associated with deafness. Hum Mutat 2019; 40:525-531. [PMID: 30740825 DOI: 10.1002/humu.23719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/23/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Otoancorin (OTOA), encoded by OTOA, is required for the development of the tectorial membrane in the inner ear. Mutations in this gene cause nonsyndromic hearing loss (DFNB22). The molecular mechanisms underlying most DFNB22 remain poorly understood. Disruption of glycosylphosphatidylinositol (GPI) anchorage has been assumed to be the pathophysiology mandating experimental validation. From a Korean deaf family, we identified two trans OTOA variants (c.1320 + 5 G > C and p.Gln589ArgfsX55 [NM_144672.3]) . The pathogenic potential of c.1320 + 5 G > C was confirmed by a minigene splicing assay. To experimentally determine the GPI anchorage, wild-type (WT) and mutant OTOA harboring p.Gln589ArgfsX55 were expressed in HEK293T cells. The mutant OTOA with p.Gln589ArgfsX55 resulted in an uncontrolled release of OTOA into the medium in contrast with phosphatidylinositol-specific phospholipase C-induced controlled release of WT OTOA from the cell surface. Together, the results of this reverse translational study confirmed GPI-anchorage of OTOA and showed that downstream sequences from the 589th amino acid are critical for GPI-anchorage.
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Affiliation(s)
- Bong Jik Kim
- Department of Otolaryngology - Head and Neck Surgery, Chungnam National University College of Medicine, Daejeon, South Korea.,Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Dong-Kyu Kim
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jin Hee Han
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jayoung Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Nayoung Kd Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Hye-Rim Park
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Min Young Kim
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Sungjin Park
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Byung Yoon Choi
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
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21
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Al-Amri AH, Al Saegh A, Al-Mamari W, El-Asrag ME, Al-Kindi MN, Al Khabouri M, Al Wardy N, Al Lamki K, Gabr A, Idris A, Inglehearn CF, Clapcote SJ, Ali M. LHFPL5 mutation: A rare cause of non-syndromic autosomal recessive hearing loss. Eur J Med Genet 2018; 62:103592. [PMID: 30476627 DOI: 10.1016/j.ejmg.2018.11.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/30/2018] [Accepted: 11/22/2018] [Indexed: 11/18/2022]
Abstract
Hearing loss is a debilitating disorder that impairs language acquisition, resulting in disability in children and potential isolation in adulthood. Its onset can have a genetic basis, though environmental factors, which are often preventable, can also cause the condition. The genetic forms are highly heterogeneous, and early detection is necessary to arrange appropriate patient support. Here we report the molecular basis of hereditary hearing loss in a consanguineous family with multiple affected members from Oman. Combining homozygosity mapping with whole exome sequencing identified a novel homozygous nucleotide substitution c.575T > C in the lipoma HMGIC fusion partner-like 5 gene (LHFPL5), that converted the 192nd amino acid residue in the protein from a leucine to a proline, p.(Leu192Pro). Sanger sequencing confirmed segregation with the disease phenotype as expected for a recessive condition and the variant was absent in 123,490 subjects from various disease-specific and population genetic studies as well as 150 unrelated individuals and 35 deaf patients of Omani ethnicity. This study, which describes a novel LHFPL5 mutation in a family of Omani origin with hereditary hearing loss, supports previous clinical descriptions of the condition and contributes to the genetic spectrum of mutations in this form of deafness.
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Affiliation(s)
- Ahmed H Al-Amri
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom; School of Biomedical Sciences, University of Leeds, United Kingdom; National Genetic Centre, Directorate General of Royal Hospital, Ministry of Health, Muscat, Oman
| | - Abeer Al Saegh
- Genetic & Developmental Medicine Clinic, Genetics Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Watfa Al-Mamari
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Mohammed E El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom; Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | | | - Mazin Al Khabouri
- Department of Ear, Nose & Throat, Al Nahdha Hospital, Ministry of Health, Muscat, Oman
| | - Nadia Al Wardy
- Biochemistry Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalsa Al Lamki
- Biochemistry Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahlam Gabr
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahmed Idris
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Chris F Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom
| | | | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Medical Research at St. James's, University of Leeds, United Kingdom.
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Liaqat K, Chiu I, Lee K, Chakchouk I, Andrade-Elizondo PB, Santos-Cortez RLP, Hussain S, Nawaz S, Ansar M, Khan MN, Basit S, Schrauwen I, Ahmad W, Leal SM. Novel missense and 3'-UTR splice site variants in LHFPL5 cause autosomal recessive nonsyndromic hearing impairment. J Hum Genet 2018; 63:1099-1107. [PMID: 30177809 PMCID: PMC6202120 DOI: 10.1038/s10038-018-0502-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
LHFPL5, the gene for DFNB67, underlies autosomal recessive nonsyndromic hearing impairment. We identified seven Pakistani families that mapped to 6p21.31, which includes the LHFPL5 gene. Sanger sequencing of LHFPL5 using DNA samples from hearing impaired and unaffected members of these seven families identified four variants. Among the identified variants, two were novel: one missense c.452 G > T (p.Gly151Val) and one splice site variant (c.*16 + 1 G > A) were each identified in two families. Two known variants: c.250delC (p.Leu84*) and c.380 A > G (p.Tyr127Cys) were also observed in two families and a single family, respectively. Nucleotides c.452G and c.*16 + 1G and amino-acid residue p.Gly151 are under strong evolutionary conservation. In silico bioinformatics analyses predicted these variants to be damaging. The splice site variant (c.*16 + 1 G > A) is predicted to affect pre-mRNA splicing and a loss of the 5' donor splice site in the 3'-untranslated region (3'-UTR). Further analysis supports the activation of a cryptic splice site approximately 357-bp downstream, leading to an extended 3'-UTR with additional regulatory motifs. In conclusion, we identified two novel variants in LHFPL5, including a unique 3'-UTR splice site variant that is predicted to impact pre-mRNA splicing and regulation through an extended 3'-UTR.
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Affiliation(s)
- Khurram Liaqat
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ilene Chiu
- Bobby R Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Imen Chakchouk
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Paula B Andrade-Elizondo
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shabir Hussain
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shoaib Nawaz
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Nasim Khan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunawwarah, Saudi Arabia
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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23
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Lerat J, Bonnet C, Cartault F, Loundon N, Jacquemont ML, Darcel F, Rouillon I, Mezouaghi K, Guichet A, Litzler J, Gesny R, Gherbi S, Aissa IB, Digeon FSJ, Garabedian EN, Bonnefont JP, Genin E, Denoyelle F, Jonard L, Marlin S. High prevalence of congenital deafness on Reunion Island is due to a founder variant of LHFPL5. Clin Genet 2018; 95:177-181. [PMID: 30298622 DOI: 10.1111/cge.13460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 11/28/2022]
Abstract
Reunion Island is a French oversea department in the Indian Ocean with 1.6/1000, an estimated prevalence of deafness that is almost double as compared to the mainland France. Twelve children having isolated bilateral prelingual profound deafness along with motor delay attributed to vestibular areflexia were enrolled. Their mean walking age was 19 months. Electroretinography and temporal bone CT-scans were normal in all cases. A novel homozygous frameshift lipoma HMGIC fusion partner-like 5 (LHFPL5) variant c.185delT p.(Phe62Serfs*23) was identified using whole-exome sequencing. It was found in seven families. Four patients from two different families from both Reunion Island and mainland France, were compound heterozygous: c.185delT p.(Phe62Serfs*23) and c.472C > T p.(Arg158Trp). The phenotype observed in our patients completely mimics the hurry-scurry (hscy) murine Tmhs knock-out model. The recurrent occurrence of same LHFPL5 variant in Reunion Island is attributed to common ancestor couple born in 1693.
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Affiliation(s)
- Justine Lerat
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Génétique Moléculaire, Necker, AP-HP, Paris, France.,Otorhinolaryngologie, CHU, Limoges, France
| | - Crystel Bonnet
- Institut de la Vision, UMRS 1120 INSERM/UPMC, Paris, France
| | - François Cartault
- Génétique Moléculaire, CHU La Réunion site Felix Guyon, Paris, France
| | - Natalie Loundon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | | | - Isabelle Rouillon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Kheira Mezouaghi
- Centre Régional de Compétences en Surdité Infantile, Sainte-Clothilde, France
| | | | | | | | - Souad Gherbi
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Ines Ben Aissa
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | | | - Eréa-Nöel Garabedian
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | - Emmanuelle Genin
- UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, CHU Brest, France
| | - Françoise Denoyelle
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Laurence Jonard
- Génétique Moléculaire, Necker, AP-HP, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Sandrine Marlin
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
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24
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Talbi S, Bonnet C, Riahi Z, Boudjenah F, Dahmani M, Hardelin JP, Wong Jun Tai F, Louha M, Ammar-Khodja F, Petit C. Genetic heterogeneity of congenital hearing impairment in Algerians from the Ghardaïa province. Int J Pediatr Otorhinolaryngol 2018; 112:1-5. [PMID: 30055715 DOI: 10.1016/j.ijporl.2018.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 01/04/2023]
Abstract
BACKGROUND Consanguinity rate is high in Algeria, and the population is thus at high risk for genetic diseases transmitted on an autosomal recessive mode. Inherited congenital hearing impairment (HI) is a highly heterogeneous disorder, which affects approximately 1 in 800 Algerian newborns. Several hundreds of genes responsible for deafness have been reported among which more than one hundred are responsible for isolated deafness, of which 19 have already been reported to be involved in the Algerian population. This study focuses on patients from the Ghardaïa province, an ethnically and geographically isolated region of Southern Algeria that has the highest consanguinity rate in the country (56%). METHODS Eleven families, with at least two related members experiencing moderate to profound congenital HI, were recruited and screened for mutations in known HI genes. RESULTS A preliminary screening for common mutations in GJB2 and GJB6 identified the prevalent GJB2:c.35delG mutation in four families. Targeted exome sequencing further identified the causal mutations in the remaining seven families: CIB2:c.97C > T; p.(Arg33*), MYO7A:c.470+1G > A; p.(?), and SLC26A4:c.410C > T; p.(Ser137Leu) biallelic mutations in two families each, and a TECTA:c.2743 A > G; p.(Ile915Val) monoallelic mutation in the only family with autosomal dominant transmission of the HI. Of note, the missense mutations of SLC26A4 and TECTA had not been previously reported. CONCLUSION These results further substantiate the genetic heterogeneity of HI, even in reportedly isolated populations. However, several families may harbor the same mutations as a result of a long history of marriages between relatives. This study has important implications for the HI molecular diagnosis strategy, and to develop genetic counseling for families originating from the Ghardaïa province of Algeria.
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Affiliation(s)
- Sonia Talbi
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène, Algiers, Algeria
| | - Crystel Bonnet
- Inserm UMRS 1120 /Institut Pasteur/Sorbonne University, Paris, France
| | - Zied Riahi
- Inserm UMRS 1120 /Institut Pasteur/Sorbonne University, Paris, France
| | - Farid Boudjenah
- ENT Department, Frantz Fanon Hospital, Bejaia, Algeria; ENT Department, Sidi Belloua Hospital, Tizi-Ouzou, Algeria
| | - Malika Dahmani
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène, Algiers, Algeria
| | | | | | - Malek Louha
- Biochemistry Department, APHP - Armand Trousseau Hospital, Paris, France
| | - Fatima Ammar-Khodja
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène, Algiers, Algeria
| | - Christine Petit
- Inserm UMRS 1120 /Institut Pasteur/Sorbonne University, Paris, France; Collège de France, Paris, France.
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25
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Carvalho SDCES, Grangeiro CHP, Picanço-Albuquerque CG, Dos Anjos TO, De Molfetta GA, Silva WA, Ferraz VEDF. Contribution of SLC26A4 to the molecular diagnosis of nonsyndromic prelingual sensorineural hearing loss in a Brazilian cohort. BMC Res Notes 2018; 11:546. [PMID: 30068397 PMCID: PMC6071330 DOI: 10.1186/s13104-018-3647-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Hereditary hearing loss (HL) is the most common sensorineural disorder in humans. Besides mutations in GJB2 and GJB6 genes, pathogenic variants in the SLC26A4 gene have been reported as a cause of hereditary HL due to its role in the physiology of the inner ear. In this research we wanted to investigate the prevalence of mutations in SLC26A4 in Brazilian patients with nonsyndromic prelingual sensorineural HL. We applied the high-resolution melting technique to screen 88 DNA samples from unrelated deaf individuals that were previously screened for GJB2, GJB6 and MT-RNR1 mutations. RESULTS The frequency of mutations in the SLC26A4 gene was 28.4%. Two novel mutations were found: p.Ile254Val and p.Asn382Lys. The mutation c.-66C>G (rs17154282) in the promoter region of SLC26A4, was the most frequent mutation found and was significantly associated with nonsyndromic prelingual sensorineural HL. After mutations in the GJB2, GJB6 and mitochondrial genes, SLC26A4 mutations are considered the next most common cause of hereditary HL in Brazilian as well as in other populations, which corroborates with our data. Furthermore, we suggest the inclusion of the SCL26A4 gene in the investigation of hereditary HL since there was an increase in the frequency of the mutations found, up to 22.7%.
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Affiliation(s)
| | - Carlos Henrique Paiva Grangeiro
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Clarissa Gondim Picanço-Albuquerque
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Thaís Oliveira Dos Anjos
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Greice Andreotti De Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Regional Blood Center of Ribeirão Preto (FUNDHERP) of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Victor Evangelista de Faria Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil. .,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil. .,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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26
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Asgharzade S, Tabatabaiefar MA, Mohammadi-Asl J, Chaleshtori MH. A novel missense mutation in GIPC3 causes sensorineural hearing loss in an Iranian family revealed by targeted next-generation sequencing. Int J Pediatr Otorhinolaryngol 2018; 108:8-11. [PMID: 29605370 DOI: 10.1016/j.ijporl.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/07/2018] [Accepted: 01/10/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND Recent studies have confirmed the utility of targeted next-generation sequencing (NGS), providing a remarkable opportunity to find variants in known disease genes, especially in genetically heterogeneous disorders such as hearing loss (HL). METHODS After excluding mutations in the most common autosomal recessive non-syndromic HL (ARNSHL) genes via Sanger sequencing and genetic linkage analysis, we performed NGS in the proband an Iranian family with ARNSHL. The NimbleGen sequence capture array captures codingsequences (CDSs) and 100 bp of the flanking sequence of 129 common deafness genes (cat# Oto-DA3). NGSwas performed on the IlluminaHiSeq2000. BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV were applied for Bioinformatics analyses. Data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFTscores (>0.95) prioritized 1indel (insertions/deletions) and 3 missense variants in this family. Eventually, Sanger sequencing, segregation pattern, the frequency in 50 healthy matched normal controls, and evolutionary conservation of amino acid residues revealed the pathogenic variant. RESULTS We identified a novel missenseGIPC3 mutation, c.472G > A (p.Glu158 Lys). The pathogenicity of GIPC3c.472G > A was supported by its absence in the population databases and the healthy-matched controls.Sanger sequencing confirmed co-segregation of the mutation with HL. CONCLUSIONS This study is the first report of the contribution of theGIPC3 gene to HL in the Iranian population.Targeted NGS allows easier detection of mutations in relatively uncommon deafness genes in families with ARNSHL.
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Affiliation(s)
- Samira Asgharzade
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Mohammadi-Asl
- Department of Medical Genetics, School of Medicine, AhvazJundishapurUniversity of Medical Sciences, Ahvaz, Iran
| | - Morteza Hashemzadeh Chaleshtori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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27
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Affiliation(s)
- Maximilian Muenke
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Suzanne Hart
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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28
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Fontana P, Morgutti M, Pecile V, Lenarduzzi S, Cappellani S, Falco M, Scarano F, Lonardo F. A novel OTOA mutation in an Italian family with hearing loss. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Bousfiha A, Bakhchane A, Charoute H, Detsouli M, Rouba H, Charif M, Lenaers G, Barakat A. Novel compound heterozygous mutations in the GPR98 (USH2C) gene identified by whole exome sequencing in a Moroccan deaf family. Mol Biol Rep 2017; 44:429-434. [PMID: 28951997 DOI: 10.1007/s11033-017-4129-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/19/2017] [Indexed: 01/26/2023]
Abstract
In the present work, we identified two novel compound heterozygote mutations in the GPR98 (G protein-coupled receptor 98) gene causing Usher syndrome. Whole-exome sequencing was performed to study the genetic causes of Usher syndrome in a Moroccan family with three affected siblings. We identify two novel compound heterozygote mutations (c.1054C > A, c.16544delT) in the GPR98 gene in the three affected siblings carrying post-linguale bilateral moderate hearing loss with normal vestibular functions and before installing visual disturbances. This is the first time that mutations in the GPR98 gene are described in the Moroccan deaf patients.
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Affiliation(s)
- Amale Bousfiha
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco.,Laboratoire des Sciences Biologiques, Filière Technique de Santé, Institution Supérieure des Professions Infirmières et Techniques de Santé (ISPITS), Casablanca, Morocco
| | - Amina Bakhchane
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Hicham Charoute
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Mustapha Detsouli
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Hassan Rouba
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Majida Charif
- PREMMI, Mitochondrial Medicine Research Centre, Université d'Angers, CHU Bât IRIS/IBS, Rue des Capucins, 49933, Angers Cedex 9, France
| | - Guy Lenaers
- PREMMI, Mitochondrial Medicine Research Centre, Université d'Angers, CHU Bât IRIS/IBS, Rue des Capucins, 49933, Angers Cedex 9, France
| | - Abdelhamid Barakat
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, 1, Place Louis Pasteur, 20360, Casablanca, Morocco.
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30
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Shang G, Brautigam CA, Chen R, Lu D, Torres-Vázquez J, Zhang X. Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex. eLife 2017; 6. [PMID: 28537552 PMCID: PMC5461112 DOI: 10.7554/elife.27322] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/23/2017] [Indexed: 12/22/2022] Open
Abstract
The GIPC family adaptor proteins mediate endocytosis by tethering cargo proteins to the myosin VI motor. The structural mechanisms for the GIPC/cargo and GIPC/myosin VI interactions remained unclear. PlexinD1, a transmembrane receptor that regulates neuronal and cardiovascular development, is a cargo of GIPCs. GIPC-mediated endocytic trafficking regulates PlexinD1 signaling. Here, we unravel the mechanisms of the interactions among PlexinD1, GIPCs and myosin VI by a series of crystal structures of these proteins in apo or bound states. GIPC1 forms a domain-swapped dimer in an autoinhibited conformation that hinders binding of both PlexinD1 and myosin VI. PlexinD1 binding to GIPC1 releases the autoinhibition, promoting its interaction with myosin VI. GIPCs and myosin VI interact through two distinct interfaces and form an open-ended alternating array. Our data support that this alternating array underlies the oligomerization of the GIPC/Myosin VI complexes in solution and cells. DOI:http://dx.doi.org/10.7554/eLife.27322.001
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Affiliation(s)
- Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rui Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Defen Lu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jesús Torres-Vázquez
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York, United States
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
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31
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Naz S, Imtiaz A, Mujtaba G, Maqsood A, Bashir R, Bukhari I, Khan MR, Ramzan M, Fatima A, Rehman AU, Iqbal M, Chaudhry T, Lund M, Brewer CC, Morell RJ, Friedman TB. Genetic causes of moderate to severe hearing loss point to modifiers. Clin Genet 2016; 91:589-598. [PMID: 27573290 DOI: 10.1111/cge.12856] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 11/30/2022]
Abstract
The genetic underpinnings of recessively inherited moderate to severe sensorineural hearing loss are not well understood, despite its higher prevalence in comparison to profound deafness. We recruited 92 consanguineous families segregating stable or progressive, recessively inherited moderate or severe hearing loss. We utilized homozygosity mapping, Sanger sequencing, targeted capture of known deafness genes with massively parallel sequencing and whole exome sequencing to identify the molecular basis of hearing loss in these families. Variants of the known deafness genes were found in 69% of the participating families with the SLC26A4, GJB2, MYO15A, TMC1, TMPRSS3, OTOF, MYO7A and CLDN14 genes together accounting for hearing loss in 54% of the families. We identified 20 reported and 21 novel variants in 21 known deafness genes; 16 of the 20 reported variants, previously associated with stable, profound deafness were associated with moderate to severe or progressive hearing loss in our families. These data point to a prominent role for genetic background, environmental factors or both as modifiers of human hearing loss severity.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Ayesha Imtiaz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.,Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Ghulam Mujtaba
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Azra Maqsood
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Rasheeda Bashir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Ihtisham Bukhari
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad R Khan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Memoona Ramzan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Amara Fatima
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Muddassar Iqbal
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Taimur Chaudhry
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Merete Lund
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Carmen C Brewer
- Audiology Unit, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892.,Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
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32
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Abdi S, Bahloul A, Behlouli A, Hardelin JP, Makrelouf M, Boudjelida K, Louha M, Cheknene A, Belouni R, Rous Y, Merad Z, Selmane D, Hasbelaoui M, Bonnet C, Zenati A, Petit C. Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome. PLoS One 2016; 11:e0161893. [PMID: 27583663 PMCID: PMC5008642 DOI: 10.1371/journal.pone.0161893] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive disorder characterized by a dual sensory impairment affecting hearing and vision. USH is clinically and genetically heterogeneous. Ten different causal genes have been reported. We studied the molecular bases of the disease in 18 unrelated Algerian patients by targeted-exome sequencing, and identified the causal biallelic mutations in all of them: 16 patients carried the mutations at the homozygous state and 2 at the compound heterozygous state. Nine of the 17 different mutations detected in MYO7A (1 of 5 mutations), CDH23 (4 of 7 mutations), PCDH15 (1 mutation), USH1C (1 mutation), USH1G (1 mutation), and USH2A (1 of 2 mutations), had not been previously reported. The deleterious consequences of a missense mutation of CDH23 (p.Asp1501Asn) and the in-frame single codon deletion in USH1G (p.Ala397del) on the corresponding proteins were predicted from the solved 3D-structures of extracellular cadherin (EC) domains of cadherin-23 and the sterile alpha motif (SAM) domain of USH1G/sans, respectively. In addition, we were able to show that the USH1G mutation is likely to affect the binding interface between the SAM domain and USH1C/harmonin. This should spur the use of 3D-structures, not only of isolated protein domains, but also of protein-protein interaction interfaces, to predict the functional impact of mutations detected in the USH genes.
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Affiliation(s)
- Samia Abdi
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Amel Bahloul
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Asma Behlouli
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Faculté des sciences biologiques, Université des sciences et de la technologie Houari Boumédiène, 16 Alger, Algérie
| | - Jean-Pierre Hardelin
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Mohamed Makrelouf
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Kamel Boudjelida
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | - Malek Louha
- Service de biochimie et de biologie moléculaire, Hôpital Armand Trousseau, APHP, 75012, Paris, France
| | - Ahmed Cheknene
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Rachid Belouni
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Yahia Rous
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Zahida Merad
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | | | | | - Crystel Bonnet
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
| | - Akila Zenati
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Christine Petit
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
- Collège de France, 75005, Paris, France
- * E-mail:
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Rehman AU, Bird JE, Faridi R, Shahzad M, Shah S, Lee K, Khan SN, Imtiaz A, Ahmed ZM, Riazuddin S, Santos-Cortez RLP, Ahmad W, Leal SM, Riazuddin S, Friedman TB. Mutational Spectrum of MYO15A and the Molecular Mechanisms of DFNB3 Human Deafness. Hum Mutat 2016; 37:991-1003. [PMID: 27375115 DOI: 10.1002/humu.23042] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/26/2016] [Indexed: 12/17/2022]
Abstract
Deafness in humans is a common neurosensory disorder and is genetically heterogeneous. Across diverse ethnic groups, mutations of MYO15A at the DFNB3 locus appear to be the third or fourth most common cause of autosomal-recessive, nonsyndromic deafness. In 49 of the 67 exons of MYO15A, there are currently 192 recessive mutations identified, including 14 novel mutations reported here. These mutations are distributed uniformly across MYO15A with one enigmatic exception; the alternatively spliced giant exon 2, encoding 1,233 residues, has 17 truncating mutations but no convincing deafness-causing missense mutations. MYO15A encodes three distinct isoform classes, one of which is 395 kDa (3,530 residues), the largest member of the myosin superfamily of molecular motors. Studies of Myo15 mouse models that recapitulate DFNB3 revealed two different pathogenic mechanisms of hearing loss. In the inner ear, myosin 15 is necessary both for the development and the long-term maintenance of stereocilia, mechanosensory sound-transducing organelles that extend from the apical surface of hair cells. The goal of this Mutation Update is to provide a comprehensive review of mutations and functions of MYO15A.
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Affiliation(s)
- Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Jonathan E Bird
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892.,Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 54550, Pakistan
| | - Mohsin Shahzad
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Sujay Shah
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Shaheen N Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 54550, Pakistan
| | - Ayesha Imtiaz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, 21201
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, University of Health Sciences, Lahore, 54550, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, 20892.
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A novel biallelic splice site mutation of TECTA causes moderate to severe hearing impairment in an Algerian family. Int J Pediatr Otorhinolaryngol 2016; 87:28-33. [PMID: 27368438 DOI: 10.1016/j.ijporl.2016.04.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/25/2016] [Accepted: 04/28/2016] [Indexed: 01/18/2023]
Abstract
Congenital deafness is certainly one of the most common monogenic diseases in humans, but it is also one of the most genetically heterogeneous, which makes molecular diagnosis challenging in most cases. Whole-exome sequencing in two out of three Algerian siblings affected by recessively-inherited, moderate to severe sensorineural deafness allowed us to identify a novel splice donor site mutation (c.5272+1G > A) in the gene encoding α-tectorin, a major component of the cochlear tectorial membrane. The mutation was present at the homozygous state in the three affected siblings, and at the heterozygous state in their unaffected, consanguineous parents. To our knowledge, this is the first reported TECTA mutation leading to the DFNB21 form of hearing impairment among Maghrebian individuals suffering from congenital hearing impairment, which further illustrates the diversity of the genes involved in congenital deafness in the Maghreb.
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Mutations in eight small DFNB genes are not a frequent cause of non-syndromic hereditary hearing loss in Czech patients. Int J Pediatr Otorhinolaryngol 2016; 86:27-33. [PMID: 27260575 DOI: 10.1016/j.ijporl.2016.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate the contribution of eight small NSHL-AR (non-syndromic deafness, autosomal recessive) genes to hereditary hearing loss in Czech patients. PATIENTS AND METHODS Unrelated Czech patients, adults and children, diagnosed with pre-lingual hereditary hearing loss with at least one similarly affected deaf sibling and with previously excluded mutations in the GJB2 gene were investigated by Sanger sequencing of the selected eight small NSHL-AR associated genes (CABP2 - 51 patients, CIB2 - 45 patients, PJVK/DFNB59 - 53 patients, GJB3 - 46 patients, ILDR1 - 48 patients, LHFPL5 - 66 patients, LRTOMT - 60 patients, TMIE - 64 patients). RESULTS Mutations were detected in the LHFPL5 (DFNB67) gene. The patient is heterozygote for two already described pathogenic variants (p.Tyr127Cys, p.Thr165Met). In five samples, five rare heterozygous variants (two novel) predicted as pathogenic were detected in genes CABP2, ILDR1, LHFPL5 and LRTOMT. CONCLUSION Mutations in eight small NSHL-AR genes are not a frequent cause of hereditary hearing loss in the Czech Republic. This diagnostic approach permitted the clarification of HL in only one patient - two heterozygous mutations were detected in LHFPL5 gene for the first time in Central Europe. As the use of panel base MPS certainly improves the diagnostic yield, future studies should rather profit from that diagnostic strategy.
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Dahmani M, Ammar-Khodja F, Bonnet C, Lefèvre GM, Hardelin JP, Ibrahim H, Mallek Z, Petit C. EPS8L2 is a new causal gene for childhood onset autosomal recessive progressive hearing loss. Orphanet J Rare Dis 2015; 10:96. [PMID: 26282398 PMCID: PMC4539681 DOI: 10.1186/s13023-015-0316-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/03/2015] [Indexed: 12/21/2022] Open
Abstract
Background More than 70 % of the cases of congenital deafness are of genetic origin, of which approximately 80 % are non-syndromic and show autosomal recessive transmission (DFNB forms). To date, 60 DFNB genes have been identified, most of which cause congenital, severe to profound deafness, whereas a few cause delayed progressive deafness in childhood. We report the study of two Algerian siblings born to consanguineous parents, and affected by progressive hearing loss. Method After exclusion of GJB2 (the gene most frequently involved in non-syndromic deafness in Mediterranean countries), we performed whole-exome sequencing in one sibling. Results A frame-shift variant (c.1014delC; p.Ser339Alafs*15) was identified in EPS8L2, encoding Epidermal growth factor receptor Pathway Substrate 8 L2, a protein of hair cells’ stereocilia previously implicated in progressive deafness in the mouse. This variant predicts a truncated, inactive protein, or no protein at all owing to nonsense-mediated mRNA decay. It was detected at the homozygous state in the two clinically affected siblings, and at the heterozygous state in the unaffected parents and one unaffected sibling, whereas it was never found in a control population of 150 Algerians with normal hearing or in the Exome Variant Server database. Conclusion Whole-exome sequencing allowed us to identify a new gene responsible for childhood progressive hearing loss transmitted on the autosomal recessive mode.
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Affiliation(s)
- Malika Dahmani
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB), El Alia, Bab-Ezzouar, Algiers, Algeria.
| | - Fatima Ammar-Khodja
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB), El Alia, Bab-Ezzouar, Algiers, Algeria.
| | - Crystel Bonnet
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France.
| | - Gaelle M Lefèvre
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France.
| | - Jean-Pierre Hardelin
- UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France. .,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015, Paris, France.
| | - Hassina Ibrahim
- Service d'otorhinolaryngologie, Centre Hospitalier Universitaire Mustapha Pacha, Algiers, Algeria.
| | - Zahia Mallek
- Service d'otorhinolaryngologie, Centre Hospitalier Universitaire Bab El Oued, Algiers, Algeria.
| | - Christine Petit
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France. .,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015, Paris, France. .,Collège de France, 75005, Paris, France.
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A novel mutation in the TMC1 gene causes non-syndromic hearing loss in a Moroccan family. Gene 2015; 574:28-33. [PMID: 26226225 DOI: 10.1016/j.gene.2015.07.075] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/29/2015] [Accepted: 07/22/2015] [Indexed: 01/28/2023]
Abstract
Autosomal recessive non-syndromic hearing loss (ARNSHL) is one of the most common genetic diseases in human and is subject to important genetic heterogeneity, rendering molecular diagnosis difficult. Whole-exome sequencing is thus a powerful strategy for this purpose. After excluding GJB2 mutation and other common mutations associated with hearing loss in Morocco, whole-exome sequencing was performed to study the genetic causes of one sibling with ARSHNL in a consanguineous Moroccan family. After filtering data and Sanger sequencing validation, one novel pathogenic homozygous mutation c.1810C>G (p.Arg604Gly) was identified in TMC1, a gene reported to cause deafness in various populations. Thus, we identified here the first mutation in the TMC1 gene in the Moroccan population causing non-syndromic hearing loss.
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