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

gnomAD frequency: 0.00006  dbSNP: rs529500747

Total submissions: 10

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 Inc	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
Natera, Inc.	RCV000988961	SCV001455334	likely pathogenic	Autosomal recessive nonsyndromic hearing loss 1A	2020-09-16	no assertion criteria provided	clinical testing