13-20189526-C-G

Variant names:

• chr13-20189526-C-G
• rs80338941
• NM_004004.6:c.56G>C

Variant summary

Our verdict is Pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2_Supporting PM3 PS3_Moderate PP1

This summary comes from the ClinGen Evidence Repository: The variant NM_004004.6:c.56G>C in GJB2 is a missense variant predicted to cause substitution of serine by threonine at amino acid 19 (p.Ser19Thr). The highest filtering allele frequency in gnomAD v4 is 0.00111% (19/1111946 CI 95%) in the non-Finnish European population (PM2_Supporting). 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 the criteria to be classified as pathogenic for autosomal recessive nonsyndromic sensorineural hearing loss, based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM3_VeryStrong, PS3_Moderate, PM2_Supporting, PP1 (ClinGen Hearing Loss VCEP specifications version 2; 1/3/24). LINK:https://erepo.genome.network/evrepo/ui/classification/CA342005/MONDO:0019497/005

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:8 U:1 O:1
• Conservation: PhyloP100: 3.30

Genes affected

GJB2 (HGNC:4284): (gap junction protein beta 2) This gene encodes a member of the gap junction protein family. The gap junctions were first characterized by electron microscopy as regionally specialized structures on plasma membranes of contacting adherent cells. These structures were shown to consist of cell-to-cell channels that facilitate the transfer of ions and small molecules between cells. The gap junction proteins, also known as connexins, purified from fractions of enriched gap junctions from different tissues differ. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene are responsible for as much as 50% of pre-lingual, recessive deafness. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Pathogenic. Variant got 6 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJB2	NM_004004.6	c.56G>C	p.Ser19Thr	missense_variant	Exon 2 of 2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.56G>C	p.Ser19Thr	missense_variant	Exon 2 of 2		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.56G>C	p.Ser19Thr	missense_variant	Exon 2 of 2	1	NM_004004.6	ENSP00000372299.4
GJB2	ENST00000382844.2	c.56G>C	p.Ser19Thr	missense_variant	Exon 1 of 1	6		ENSP00000372295.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000120 AC: 3 AN: 249778 Hom.: 0 AF XY: 0.0000148 AC XY: 2 AN XY: 135146

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000268

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000150 AC: 22 AN: 1461822 Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12 AN XY: 727214

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000171

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000312 Hom.: 0

ExAC AF: 0.0000165 AC: 2

EpiCase AF: 0.000109

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:3

Jan 08, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Jan 13, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate the p.S19T variant results in near total loss of function for gap-junction channels (D'Andrea et al., 2002); Observed multiple times with a pathogenic variant in unrelated patients in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Shen et al., 2019; Buonfiglio et al., 2020; Dalamon et al., 2013); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16077952, 26553399, 12176036, 33096615, 16380907, 35457072, 19230829, 11439000, 10982180, 19285578, 15070423, 25388846, 15146474, 24158611, 31160754, 16950989) -

Aug 21, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 19 of the GJB2 protein (p.Ser19Thr). This variant is present in population databases (rs80338941, gnomAD 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). 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) 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: 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. -

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:1 Uncertain:1 Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

May 10, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GJB2 c.56G>C (p.Ser19Thr) results in a conservative amino acid change located in the Connexin, N-terminal (IPR013092) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 249778 control chromosomes (gnomAD). c.56G>C has been reported in the literature in individuals affected with Autosomal Recessive Hearing Loss (examples: Gangarossa_2005, Buonfiglio_2020). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence that this variant affects the normal function of the protein (DAndrea_2002). The following publications have been ascertained in the context of this evaluation (PMID: 16077952, 33096615, 12176036). ClinVar contains an entry for this variant (Variation ID: 21389). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

May 09, 2017

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nonsyndromic genetic hearing loss Pathogenic:2

Aug 21, 2020

INGEBI, INGEBI / CONICET

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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) -

Jan 03, 2024

ClinGen Hearing Loss Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The variant NM_004004.6:c.56G>C in GJB2 is a missense variant predicted to cause substitution of serine by threonine at amino acid 19 (p.Ser19Thr). The highest filtering allele frequency in gnomAD v4 is 0.00111% (19/1111946 CI 95%) in the non-Finnish European population (PM2_Supporting). 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 the criteria to be classified as pathogenic for autosomal recessive nonsyndromic sensorineural hearing loss, based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM3_VeryStrong, PS3_Moderate, PM2_Supporting, PP1 (ClinGen Hearing Loss VCEP specifications version 2; 1/3/24). -

Hearing loss Pathogenic:1

Dec 01, 2006

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Rare genetic deafness Pathogenic:1

Jun 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.090
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.76	D;D;D
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.52	.;.;T
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.91	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.2	M;M;M
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-1.6	N;N;.
REVEL	Uncertain	0.63
Sift	Benign	0.31	T;T;.
Sift4G	Benign	0.062	T;T;.
Polyphen		0.46	P;P;P
Vest4		0.43
MutPred		0.83		Gain of ubiquitination at K22 (P = 0.0817);Gain of ubiquitination at K22 (P = 0.0817);Gain of ubiquitination at K22 (P = 0.0817);
MVP		0.94
MPC		0.14
ClinPred		0.47	T
GERP RS		5.2
Varity_R		0.68
gMVP		0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs80338941; hg19: chr13-20763665; COSMIC: COSV67010547; COSMIC: COSV67010547;