ClinVar Genomic variation as it relates to human health

The c.583G>C is a missense variant predicted to cause a substitution of methionine by valine at amino acid 195 (p.Met195Val). The highest population minor allele frequency in gnomAD v4.1.0 is 0.022% (16/44880, CI 95%) in the East Asian population (PM2_Supporting, BS1, and BA1 are not met). This variant has been detected in 4 individuals with hearing loss with another pathogenic or suspected-pathogenic variant found in trans (4 PM3 points PMIDs: 24013081, 20497192, 30146550,33597575) (PM3_VeryStrong). It has also been identified in several probands with hearing loss in whom a second variant was not identified (PMIDs: 23555729, 19366456, 19125024, 27627659, 24507663). The computational predictor REVEL gives a score of 0.962 which is above the threshold of 0.7, evidence that correlates with impact to GJB2 function (PP3). Analysis in Hela cells demonstrated that the CX26-p.Met195Val protein was not transported to the cell membrane since there is an accumulation of the protein in the endoplasmic reticulum, indicating that this variant impacts protein function (PMID:26749107; PS3_Moderate). In summary, this variant meets the criteria to be classified as pathogenic for autosomal recessive non-syndromic hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP (PP3, PM3_VeryStrong, PS3_Moderate; Version 2; 5/15/24).

The variant is observed at an allele frequency greater than expected for the associated disorder in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 26749107). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.96; 3Cnet: 0.99). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000225375). The variant has been observed in at least four similarly affected unrelated individuals (PMID: 19125024, 19366456, 21366436, 23555729). A different missense change at the same codon (p.Met195Ile) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000438621 , VCV001334161 , VCV001479826). The variant is in trans with the other pathogenic variants (PMID: 19125024,24507663,30146550). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 195 of the GJB2 protein (p.Met195Val). This variant is present in population databases (rs532203068, gnomAD 0.02%). This missense change has been observed in individuals with autosomal recessive GJB2-related conditions (PMID: 20497192, 24013081, 30146550, 33597575). This variant has been reported in individual(s) with autosomal dominant GJB2-related conditions (PMID: 19125024, 19366456, 21366436, 23555729); however, the role of the variant in this condition is currently unclear. ClinVar contains an entry for this variant (Variation ID: 225375). 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 with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GJB2 function (PMID: 26749107). This variant disrupts the p.Met195 amino acid residue in GJB2. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Variant summary: GJB2 c.583A>G (p.Met195Val) results in a conservative amino acid change located in the Connexin domain (IPR013092) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251340 control chromosomes. c.583A>G has been reported in the literature in multiple individuals affected with Non-Syndromic AR (example, Tsukada_2010,Wang_2021,Minami_2013 ) and AD Hearing Loss (example, Yu_2020, Batissoco_2009). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in full retention in cytoplasm (Kim_2016). The following publications have been ascertained in the context of this evaluation (PMID: 19125024, 24013081, 20497192, 33597575, 31992338). ClinVar contains an entry for this variant (Variation ID: 225375). Based on the evidence outlined above, the variant was classified as pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with both deafness and skin conditions (OMIM). Dominant negative is also a suggested mechanism (PMID: 28428247). (I) 0108 - This gene is associated with both recessive and dominant disease. The autosomal dominant diseases are commonly associated with pathogenic missense variants. The autosomal recessive disease is associated with bi-allelic loss-of-function variants and includes missense and protein truncating variants (NIH Genetics Home Reference, PMID: 12792423). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID:31160754). (I) 0115 - Variants in this gene are known to have variable expressivity. Severity can range from mild to profound with intrafamilial variability also commonly seen. Commonly, truncating variants are associated to a more severe hearing loss (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from methionine to valine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 (8 heterozygotes, 0 homozygotes). (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (v2) (highest allele count: 27 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and very highly conserved with a minor amino acid change. (SP) 0600 - Variant is located in the annotated Connexin domain (DECIPHER). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic by an expert panel and associated with autosomal recessive nonsyndromic hearing loss (ClinVar). However, it has also been classified as pathogenic in the Deafness Variation database. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The GJB2 c.583A>G variant is predicted to result in the amino acid substitution p.Met195Val. This variant has been reported in the compound heterozygous state in multiple individuals with hearing loss (Tsukada et al. 2010. PubMed ID: 20497192; Wang et al. 2021. PubMed ID: 33597575; Minami et al. 2013. PubMed ID: 24013081). This variant is reported in 0.022% of alleles in individuals of East Asian descent in gnomAD and is interpreted as likely pathogenic by the ClinGen Hearing Loss Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/225375/). This variant is interpreted as likely pathogenic.