ClinVar Genomic variation as it relates to human health

The c.428 G>A (p.R143Q) variant in the GJB2 gene has been reported previously in the compound heterozygous state in multiple unrelated individuals with congenital, profound, non-syndromic, sensorineural deafness; however, c.428 G>A has also been reported in the heterozygous state in both mildly affected and unaffected relatives of these individuals, indicating that this variant may exhibit autosomal dominant inheritance with incomplete penetrance, but also result in severe hearing loss when present in trans with an autosomal recessive GJB2 variant (Loffler et al., 2001; Bonyadi et al., 2009; Huang et al., 2013; Riahi et al., 2013). The c.428 G>A variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In-silico splice models predict that c.428 G>A may create a cryptic splice acceptor site that could supplant the natural splice acceptor site for intron 1. However, in the absence of RNA/functional studies, the actual effect of the c.428 G>A change in this individual is unknown. If c.428 G>A does not alter splicing, it will result in the R143Q missense change. The R143Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties, and this substitution occurs at a position that is conserved across species. Functional studies of the R143Q missense variant have demonstrated that this variant can participate in forming gap junctions, but the resulting channels exhibit both impaired function and permeability (Yum et al., 2010; Zhang et al., 2011). We interpret c.428 G>A (p.R143Q) as a pathogenic variant.

Variant summary: The GJB2 c.428G>A (p.Arg143Gln) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant is absent in 125474 control chromosomes. The variant has been reported in affected individuals in the heterozygous state, suggesting a dominant role of the variant. However, compound heterozygotes have been reported who have severe/profound hearing loss, indicating a more severe phenotype than individuals with only one variant. The variant was shown to co-segregate with disease in multiple families, with the exception of an affected indivdual not carrying the variant (Loffler_2001), and one unaffected family member in each study carrying the variant, suggestive of incomplete penetrance (Riahi_2013, Bonyadi_2009). One database classified this variant as pathogenic. In addition, p.Phe142Leu, p.Arg143Trp, p.Arg143Leu have been reported to associate with NSHL, suggesting Phe142-Arg143 is a mutation hot-spot. Taken together, this variant is classified as pathogenic.

The c.428G>A variant is classified as a PATHOGENIC variant (PS2, PS3, PS4, PP3, PP5) This variant is a single nucleotide change from a guanine to a adenine at position 428 which is predicted to change the arginine at position 143 to glutamine. The variant is in exon 2 and is located in Connexin protein domain of the GJB2 gene. The variant has been reported in the heterozygous state in multiple individuals, and in several families segregating with high frequency hearing loss, indicating a dominant effect of this mutation in hearing loss. This variant cam also results in severe hearing loss when present in the compound heterozygous state (PMID: 11313763, 23856378, 22991996). The variant is in dbSNP (rs104894401) but is absent from population databases (PS4). Functional studies have shownthat this variant can inhibit the transfer of calcein in cells stably expressing the gap junction protein connexin 26 (Cx26), demonstrating that the dominant negative effect of this variant on wild type Cx26 (PMID: 21040787) (PS3). Previous parental testing on the GJB2 gene has confirmed that this is a De novo variant in the patient (MG WCH report: #41493 & #41494, reported date: 17/04/2014) (PS2). The variant has been reported in ClinVar (Variation ID: 17017) and HGMD (Accession: CM010311) as pathogenic (PP5). Computational predictions support a deleterious effect on the gene or gene product (PP3).

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg143 amino acid residue in GJB2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9393973, 15235031, 15365987, 15617546, 18941476, 19715472). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects GJB2 function (PMID: 20096356, 21040787). 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. ClinVar contains an entry for this variant (Variation ID: 17017). This missense change has been observed in individual(s) with autosomal dominant deafness with incomplete penetrance and/or autosomal recessive deafness (PMID: 11313763, 22991996, 25752103, 31379920). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 143 of the GJB2 protein (p.Arg143Gln).