Submissions for variant NM_004004.6(GJB2):c.23C>T (p.Thr8Met)

gnomAD frequency: 0.00006  dbSNP: rs529500747

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Hearing Loss Variant Curation Expert Panel	RCV001257044	SCV003800589	uncertain significance	Nonsyndromic genetic hearing loss	2022-10-31	reviewed by expert panel	curation	The c.23C>T variant in GJB2 is a missense variant predicted to cause substitution of threonine by methionine at amino acid 8. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002511 (13/30616 alleles with no homozygotes) in the South Asian population (no population codes met). The computational predictor REVEL gives a score of 0.632, which is neither above nor below the thresholds predicting a damaging or benign impact on GJB2 function. Dual whole cell voltage clamp and dye transfer assays in HeLa cells demonstrated that even though potassium permeability remains the same in the variant, there is a reduction in cationic and large molecules dye transfer compared to WT (PMID:18684989) (PS3_Supporting). This variant has been detected in at least two individuals with autosomal recessive NSHL. One was compound heterozygous for the variant and a pathogenic variant, c.109G>A (p.Val37Ile), with phase unknown (0.5 PM3 points, PMID: 22384008). One individual was homozygous for the variant (0.5 PM3 points, PMID: 31162818) (PM3). In summary, this variant meets the criteria to be classified as uncertain significance for autosomal recessive nonsyndromic genetic hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM3, PS3_Supporting (Hearing Loss VCEP specifications version 2; 10/31/2022).
GeneDx	RCV000429597	SCV000517380	likely pathogenic	not provided	2021-04-12	criteria provided, single submitter	clinical testing	Reported previously in the heterozygous state in multiple individuals with hearing loss, most commonly in cis with the V153I variant, which has been suggested to be benign (Kenna et al., 2001; Dalamon et al., 2005; Snoeckx et al., 2005; Primignani et al., 2009; Bonyadi et al., 2014; Amorini et al., 2015; Burke et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27792752, 12172394, 25388846, 15241677, 18684989, 11556849, 15964725, 26778469, 15954104, 26178431, 24529908, 20497192, 19371219, 22384008, 26096904, 29605365, 29542069, 30730013, 26188157, 31162818, 30275481, 33096615)
Mendelics	RCV000988961	SCV001138913	uncertain significance	Autosomal recessive nonsyndromic hearing loss 1A	2019-05-28	criteria provided, single submitter	clinical testing
Athena Diagnostics	RCV000429597	SCV001143662	likely pathogenic	not provided	2018-09-28	criteria provided, single submitter	clinical testing	The best available variant frequency is uninformative because it is below the disease allele frequency. Statistically enriched in patients compared to ethnically matched controls. Conflicting predictions of the effect on the protein. Damaging to protein function(s) relevant to disease mechanism.
CeGaT Center for Human Genetics Tuebingen	RCV000429597	SCV001148929	likely pathogenic	not provided	2021-10-01	criteria provided, single submitter	clinical testing
INGEBI, INGEBI / CONICET	RCV001257044	SCV001433595	uncertain significance	Nonsyndromic genetic hearing loss	2020-08-31	criteria provided, single submitter	clinical testing	Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of the c.23C>T, p.Thr8Met variant in GJB2 gene is 0,025% (13/30616 South Asian alleles with 95%CI) from Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/) which meets the criteria to apply to PM2_Supporting. Functional studies in HeLa cells using dual whole cell voltage clamp and dye transfer assay demonstrated that even though potassium permeability remains the same in CX26 mutant, there is a reduction in cationic and large molecules dye transfer compared to WT (PMID:18684989). Hence PS3 criteria was downgraded to Supporting strength: PS3_Supporting. This variant has been identified several times with the benign variant p.Val153Ile suggesting that both variants are in cis phase (PMID: 24529908, 11556849, 26096904 and 24158611). The c.23C>T variant has been identified once in homozygous state and with p.Val37Ile variant with unknown phase in patients with hearing loss (PMID: 31162818, 22384008; PM3). Computational evidence did not suggest a relevant impact of the mutation to the protein (REVEL: 0,632), neither PP3 nor BP4 rules applied. In summary, the clinical significance of this variant is currently uncertain (PM2_Supporting, PS3_Supporting, PM3).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001420843	SCV001623245	uncertain significance	not specified	2022-04-05	criteria provided, single submitter	clinical testing	Variant summary: GJB2 c.23C>T (p.Thr8Met) results in a non-conservative amino acid change located in the Connexin, N-terminal 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 8e-05 in 250080 control chromosomes, predominantly at a frequency of 0.00042 within the South Asian subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in GJB2 causing Non-Syndromic Hearing Loss (8e-05 vs 0.026), allowing no conclusion about variant significance. c.23C>T has been widely reported in the literature in individuals affected with Non-Syndromic Hearing Loss ranging from severe profound bilateral (example, Dalamon_2005), moderate high frequency (example, Wu_2002) and mixed with moderate (example, Kenna_2001). In a cross sectional review of the associated literature, this variant was predominantly reported along with a benign/likely benign variant, namely p.Val153Ile in hearing loss cohorts (example, Dalamon_2005, Wu_2002, Kenna_2001, Chaleshtori_2005, Snoeckx_2005, Tsukada_2010, Primignani_2009). Although the phase of these variants was not explicitly specified in most studies, one report of the occurrence of these two variants in cis was ascertained (example, Primignani_2009). Therefore, the predominantly reported genotypes are considered as uninformative in the setting of autosomal recessive non syndromic hearing loss (ARNSHL). At-least one report of this variant in homozygosity in an individual from a cohort of ARNSHL was ascertained in this evaluation (Naddafnia_2018). Recently, a study evaluating this variant utilizing the hearing-loss-gene-specific criteria of the ClinGen Hearing Loss Expert Panel classified the variant as a VUS (example, Buonfiglio_2020). Overall, these data indicate that the variant may be associated with disease, but do not provide an unequivocal association with hearing loss. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant on targeting to cell membrane, mean junctional and unitary conductance although an altered permeability to large cationic molecules such as ethidium bromide was reported (Mese_2008). However, the exact in-vivo consequences of these findings on the pathophysiology of hearing loss is not clear. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (likely pathogenic, n=6; VUS, n=2). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as a VUS-possibly pathogenic.
Pars Genome Lab	RCV000988961	SCV001652838	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 1A	2021-05-18	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000988961	SCV001810446	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 1A	2021-07-22	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000988961	SCV005399529	uncertain significance	Autosomal recessive nonsyndromic hearing loss 1A	2022-02-02	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. 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. 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 threonine to methionine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (22 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated connexin domain (DECIPHER). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. It has been reported both as VUS and likely pathogenic in ClinVar. Although the Deafness Variation Database regards it as pathogenic, the classification of this variant is also conflicting in the literature and has been recently classified as VUS by a review using ACMG and ClinGen expert guidelines (PMID: 33096615). It has been detected both in healthy and affected individuals (PMIDs: 26178431, 31162818). (I) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Dual whole cell patch clamp and dye flux experiments in transfected HeLa cells found that mutant localisation was not impaired and that wild-type and mutant showed comparable ionic coupling, as well as cAMP and LY permeability. However, the transfer of ethidium bromide was greatly reduced in mutants suggesting impaired permeability to large cationic molecules (PMID: 18684989). The biological and clinical significance of these results are unclear. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Labcorp Genetics (formerly Invitae), Labcorp	RCV000429597	SCV005734232	uncertain significance	not provided	2025-01-06	criteria provided, single submitter	clinical testing	This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 8 of the GJB2 protein (p.Thr8Met). This variant is present in population databases (rs529500747, gnomAD 0.04%). This missense change has been observed in individual(s) with GJB2-related conditions (PMID: 22384008, 26095810, 31162818, 36147510). ClinVar contains an entry for this variant (Variation ID: 379889). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GJB2 protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GJB2 function (PMID: 15241677, 18684989). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Natera, Inc.	RCV000988961	SCV001455334	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 1A	2020-09-16	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004735511	SCV005361440	uncertain significance	GJB2-related disorder	2024-06-06	no assertion criteria provided	clinical testing	The GJB2 c.23C>T variant is predicted to result in the amino acid substitution p.Thr8Met. This variant has been reported in the heterozygous state in individuals with non-syndromic hearing loss (NSHL) (Buonfiglio et al. 2020. PubMed ID: 33096615; Adhikary et al. 2015. PubMed ID: 26188157) and mixed hearing loss (Kenna et al. 2001. PubMed ID: 11556849). It has been reported in the homozygous state in one individual with NSHL (Naddafnia et al. 2019. PubMed ID: 31162818). This variant has also been reported in an individual with severe hearing loss; however, it was considered a variant of uncertain significance (Gao et al. 2016. PubMed ID: 27792752) and has been reported in two unaffected individuals (Quaio et al. 2022. PubMed ID: 36147510). Functional studies found this variant retains the ability to form gap junction channels but at lower conductance levels and with abnormal gating properties (Meşe et al. 2004. PubMed ID: 15241677). This variant is reported in 0.042% of alleles in individuals of South Asian descent in gnomAD. It is interpreted as uncertain by the ClinGen Hearing Loss Variant Curation Expert Panel in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/379889/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.