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Vanniya S P, Chandru J, Jeffrey JM, Rabinowitz T, Brownstein Z, Krishnamoorthy M, Avraham KB, Cheng L, Shomron N, Srisailapathy CRS. PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India. Ann Hum Genet 2021; 86:1-13. [PMID: 34374074 DOI: 10.1111/ahg.12442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
The study was conducted between 2018 and 2020. From a cohort of 113 hearing impaired (HI), five non-DFNB12 probands identified with heterozygous CDH23 variants were subjected to exome analysis. This resolved the etiology of hearing loss (HL) in four South Indian assortative mating families. Six variants, including three novel ones, were identified in four genes: PNPT1 p.(Ala46Gly) and p.(Asn540Ser), MYO15A p.(Leu1485Pro) and p.(Tyr1891Ter), PTPRQ p.(Gln1336Ter), and SLC12A2 p.(Pro988Ser). Compound heterozygous PNPT1 variants were associated with DFNB70 causing prelingual profound sensorineural hearing loss (SNHL), vestibular dysfunction, and unilateral progressive vision loss in one family. In the second family, MYO15A variants in the myosin motor domain, including a novel variant, causing DFNB3, were found to be associated with prelingual profound SNHL. A novel PTPRQ variant was associated with postlingual progressive sensorineural/mixed HL and vestibular dysfunction in the third family with DFNB84A. In the fourth family, the SLC12A2 novel variant was found to segregate with severe-to-profound HL causing DFNA78, across three generations. Our results suggest a high level of allelic, genotypic, and phenotypic heterogeneity of HL in these families. This study is the first to report the association of PNPT1, PTPRQ, and SLC12A2 variants with HL in the Indian population.
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Affiliation(s)
- Paridhy Vanniya S
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India.,LifeBytes India Pvt. Ltd., Bengaluru, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Tom Rabinowitz
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mathuravalli Krishnamoorthy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Le Cheng
- BGI Genomics, Shenzhen, P. R. China
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
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Kalaimathi M, Subathra M, Jeffrey JM, Selvakumari M, Chandru J, Sharanya N, Paridhy VS, Srisailapathy CRS. Low incidence of GIPC3 variants among the prelingual hearing impaired from southern India. J Genet 2020; 99:74. [PMID: 33168789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The broad spectrum of causal variants in the newly discovered GIPC3 gene is well reflected in worldwide studies. Except for one missense variant, none of the reported variants had reoccurred, thus reflecting the intragenic heterogeneity. We screened all the six coding exons of GIPC3 gene in a large cohort of 177 unrelated prelingual hearing impaired after excluding the common GJB2, GJB6 nuclear and A1555G mitochondrial variants. We observed a single homozygous pathogenic frameshift variant c.685dupG (p.A229GfsX10), accounting for a low incidence (0.56%) of GIPC3 variants in south Indian population. GIPC3 being a rare gene as a causative for deafness, the allelic spectra perhaps became much more diverse from population to population, thus resulting in a minimal recurrence of the variants in our study, that were reported by authors from other parts of the globe.
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Affiliation(s)
- Murugesan Kalaimathi
- Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai 600 113, India.
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Jeffrey JM, Chandru J, Pavithra A, Kalaimathi M, Indhumathi N, Ashraf P, Srikumari Srisailapathy CR. Exclusion of Putative <i>CATSPER2</i> and <i>STRC</i> Gene Deletion and <i>FOXI1</i> Gene Mutations in a Unique Cohort with Sensorineural Deafness and Male Infertility from South India. CURR SCI INDIA 2018. [DOI: 10.18520/cs/v114/i12/2538-2542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Amritkumar P, Jeffrey JM, Chandru J, Vanniya S P, Kalaimathi M, Ramakrishnan R, Karthikeyen NP, Srikumari Srisailapathy CR. Role of DFNB1 mutations in hereditary hearing loss among assortative mating hearing impaired families from South India. BMC Med Genet 2018; 19:105. [PMID: 29921236 PMCID: PMC6008914 DOI: 10.1186/s12881-018-0609-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/18/2018] [Indexed: 08/14/2023]
Abstract
Background DFNB1, the first locus to have been associated with deafness, has two major genes GJB2 & GJB6, whose mutations have played vital role in hearing impairment across many ethnicities in the world. In our present study we have focused on the role of these mutations in assortative mating hearing impaired families from south India. Methods One hundred and six assortatively mating hearing impaired (HI) families of south Indian origin comprising of two subsets: 60 deaf marrying deaf (DXD) families and 46 deaf marrying normal hearing (DXN) families were recruited for this study. In the 60 DXD families, 335 members comprising of 118 HI mates, 63 other HI members and 154 normal hearing members and in the 46 DXN families, 281 members comprising of 46 HI and their 43 normal hearing partners, 50 other HI members and 142 normal hearing family members, participated in the molecular study. One hundred and sixty five (165) healthy normal hearing volunteers were recruited as controls for this study. All the participating members were screened for variants in GJB2 and GJB6 genes and the outcome of gene mutations were compared in the subsequent generation in begetting deaf offspring. Results The DFNB1 allele frequencies for DXD mates and their offspring were 36.98 and 38.67%, respectively and for the DXN mates and their offspring were 22.84 and 24.38%, respectively. There was a 4.6% increase in the subsequent generation in the DXD families, while a 6.75% increase in the DXN families, which demonstrates the role of assortative mating along with consanguinity in the increase of DFNB1 mutations in consecutive generations. Four novel variants, p.E42D (in GJB2 gene), p.Q57R, p.E101Q, p.R104H (in GJB6 gene) were also identified in this study. Conclusion This is the first study from an Indian subcontinent reporting novel variants in the coding region of GJB6 gene. This is perhaps the first study in the world to test real-time, the hypothesis proposed by Nance et al. in 2000 (intense phenotypic assortative mating mechanism can double the frequency of the commonest forms of recessive deafness [DFNB1]) in assortative mating HI parental generation and their offspring.
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Affiliation(s)
- Pavithra Amritkumar
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India.,Current affiliation: PG and Research Department of Biotechnology, Women's Christian College, Chennai, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Paridhy Vanniya S
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - M Kalaimathi
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India
| | - Rajagopalan Ramakrishnan
- Department of ENT, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, India
| | - N P Karthikeyen
- DOAST Hearing Care Center, Anna Nagar, Chennai, 600040, India
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, India.
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Pavithra A, Chandru J, Jeffrey JM, Karthikeyen NP, Srisailapathy CRS. Rare compound heterozygosity involving dominant and recessive mutations of GJB2 gene in an assortative mating hearing impaired Indian family. Eur Arch Otorhinolaryngol 2016; 274:119-125. [PMID: 27481527 DOI: 10.1007/s00405-016-4229-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Connexin 26 (Cx-26), a gap junction protein coded by GJB2 gene, plays a very important role in recycling of potassium ions, one of the vital steps in the mechanotransduction process of hearing. Mutations in the GJB2 gene have been associated with both autosomal recessive as well as dominant nonsyndromic hearing loss. As Cx-26 is linked with skin homeostasis, mutations in this gene are sometimes associated with syndromic forms of hearing loss showing skin anomalies. We report here a non consanguineous assortatively mating hearing impaired family with one of the hearing impaired partners, their hearing impaired sibling and hearing impaired offspring showing compound heterozygosity in the GJB2 gene, involving a dominant mutation p.R184Q and two recessive mutations p.Q124X and c.IVS 1+1G>A in a unique triallelic combination. To the best of our knowledge, this is the first report from India on p.R184Q mutation in the GJB2 gene associated with rare compound heterozygosity showing nonsyndromic presentation.
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Affiliation(s)
- Amritkumar Pavithra
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600113, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600113, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600113, India
| | | | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600113, India.
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Pavithra A, Jeffrey JM, Chandru J, Ramesh A, Srisailapathy CRS. High incidence of GJB2 gene mutations among assortatively mating hearing impaired families in Kerala: future implications. J Genet 2014; 93:207-13. [PMID: 24840842 DOI: 10.1007/s12041-014-0338-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Amritkumar Pavithra
- Department of Genetics, Dr ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai 600 113, India.
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