ClinVar Miner

Submissions for variant NM_004004.6(GJB2):c.56G>C (p.Ser19Thr)

dbSNP: rs80338941
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Hearing Loss Variant Curation Expert Panel RCV001257035 SCV002520695 likely pathogenic Nonsyndromic genetic hearing loss 2019-07-28 reviewed by expert panel curation The filtering allele frequency for c.56G>C (p.Ser19Thr) is .000007% (3/112070 CI 95%) in non-Finnish European chromosomes in gnomAD, which is a low enough frequency to apply PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss (PM2). This variant has been detected in 5 probands with hearing loss. For 4 of those probands, a pathogenic or suspected-pathogenic variants was observed in trans (PM3_VeryStrong; PMIDs: 16077952, 26553399, 10982180, 15146474, Partners Laboratory for Molecular Medicine internal data). Of note, 1 proband was compound-heterozygous for Ser19Thr with c.35delG and also carried Arg32Ser in cis; another proband had Ser19Thr, Arg32Ser and E47* in unspecified zygosity though it is assumed that Ser19Thr and Arg32Ser were in cis based on prior observation. These cases were not counted towards PM3 because contribution of the Arg32Ser variant can not be ruled out. The p.Ser19Thr variant has been reported to segregate with hearing loss in one affected family member (PP1, PMID: 16077952). A functional study has shown that p.Ser19Thr impacts protein function (PS3_Moderate; PMID: 12176036). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive nonsyndromic sensorineural hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM2, PM3_Strong, PP1, PS3_Moderate.
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000020575 SCV000599725 uncertain significance Autosomal recessive nonsyndromic hearing loss 1A 2017-05-09 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000602210 SCV000710858 likely pathogenic Rare genetic deafness 2016-06-28 criteria provided, single submitter clinical testing The p.Ser19Thr variant in GJB2 has been reported in 4 individuals with hearing l oss, 3 of whom were compound heterozygous for a second pathogenic variant in GJB 2, and segregated in one affected family member (Rabionet 2000, Roux 2004, Toth 2004, Gangarossa 2005). This variant has been identified in 2/66716 European chr omosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.o rg; dbSNP rs80338941); however, its frequency is low enough to be consistent wit h a recessive carrier frequency. In vitro functional studies suggest that the p. Ser19Thr variant may impact protein function (D'Andrea 2002). However, these typ es of assays may not accurately represent biological function. In summary, alth ough additional studies are required to fully establish its clinical significanc e, this variant is likely pathogenic for autosomal recessive hearing loss based on the previously reported compound heterozygous individuals.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000757333 SCV000885517 likely pathogenic not provided 2018-01-08 criteria provided, single submitter clinical testing The GJB2 c.56G>C; p.Ser19Thr variant (rs80338941) has been reported in individuals with hearing loss and has been found in trans with the pathogenic 35delG variant (D'Andrea 2002, Putcha 2007, Rabionet 2000). Functional studies show the variant protein has normal expression but is unable to form functional gap-junction channels in HeLa cells (D'Andrea 2002). This variant is reported in ClinVar (Variation ID: 21389) and observed in the general population with an overall allele frequency of 0.001% (3/244518 alleles) in the Genome Aggregation Database. Based on the above information, this variant is considered likely pathogenic. REFERENCES D'Andrea P et al. Hearing loss: frequency and functional studies of the most common connexin26 alleles. Biochem Biophys Res Commun. 2002 Aug 23;296(3):685-91. Putcha GV et al. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. Genet Med. 2007 Jul;9(7):413-26. Rabionet R et al. Molecular basis of childhood deafness resulting from mutations in the GJB2 (connexin 26) gene. Hum Genet. 2000 Jan;106(1):40-4.
Invitae RCV000757333 SCV001415840 pathogenic not provided 2021-09-11 criteria provided, single submitter clinical testing This sequence change replaces serine with threonine at codon 19 of the GJB2 protein (p.Ser19Thr). The serine residue is highly conserved and there is a small physicochemical difference between serine and threonine. This variant is present in population databases (rs80338941, ExAC 0.003%). This missense change has been observed in individuals with non-syndromic deafness (PMID: 10982180, 15146474, 16077952, 24158611). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 21389). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GJB2 protein function. Experimental studies have shown that this missense change affects GJB2 function (PMID: 12176036). This variant disrupts the p.Ser19 amino acid residue in GJB2. Other variant(s) that disrupt this residue have been observed in individuals with GJB2-related conditions (PMID: 26188157), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
INGEBI, INGEBI / CONICET RCV001257035 SCV001433540 pathogenic Nonsyndromic genetic hearing loss 2020-08-21 criteria provided, single submitter clinical testing Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the c.56G>C, p.Ser19Thr variant has been found only in European non-finish population with a filtering allele frequency of 0,00072% (3/112070 chromosomes with 95% CI) from gnomAD v2.1.1 database meeting PM2 criteria. This variant has been identified in trans with pathogenic variants in at least 4 individuals with hearing impairment (PMID: 10982180, 15146674,24158611,16077952) applying to PM3_VeryStrong criteria. Besides, p.Ser19Thr change in trans with p.Met34Thr variant segregated in two affected siblings (PMID:16077952), so PP1_Moderate rule applied. Functional analysis in HeLa cells demonstrated a deleterious effect of the variant since no dye transfer was observed in mutant (PMID: 12176036) applying to PS3_Moderate rule. Therefore, the c.56G>C variant meets criteria to be classified as pathogenic for autosomal recessive non-syndromic hearing loss (PM2, PM3_VeryStrong, PP1_Moderate and PS3_Moderate)
GeneReviews RCV002286406 SCV000041051 not provided Autosomal recessive nonsyndromic hearing loss 1A no assertion provided literature only
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital RCV000678862 SCV000805055 pathogenic Hearing loss 2006-12-01 no assertion criteria provided clinical testing

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