rs80338949

chr13-20189095-T-Cchr13-20189095-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM5 BP4_Moderate

The NM_004004.6(GJB2):c.487A>G(p.Met163Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000929 in 1,614,088 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M163T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000091 (1 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:9 O:1
• Conservation: PhyloP100: 6.20

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 Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 7 uncertain in NM_004004.6
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-20189095-T-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.22010407).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.487A>G	p.Met163Val	missense_variant	2/2	ENST00000382848.5
GJB2	XM_011535049.3	c.487A>G	p.Met163Val	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.487A>G	p.Met163Val	missense_variant	2/2	1	NM_004004.6	P1
GJB2	ENST00000382844.2	c.487A>G	p.Met163Val	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 17 AN: 152182 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000143 AC: 36 AN: 251140 Hom.: 0 AF XY: 0.000192 AC XY: 26 AN XY: 135762

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.0000993

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000752

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000881

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000910 AC: 133 AN: 1461788 Hom.: 1 Cov.: 33 AF XY: 0.000120 AC XY: 87 AN XY: 727176

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.000881

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000306

Gnomad4 OTH exome AF: 0.000232

GnomAD4 genome AF: 0.000112 AC: 17 AN: 152300 Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10 AN XY: 74472

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000975 Hom.: 0

Bravo AF: 0.000159

ExAC AF: 0.000165 AC: 20

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000327

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:9 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2023	GJB2: PS4:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 09, 2023	Observed in the heterozygous state with no other GJB2 variant in multiple individuals with hearing loss in published literature (Hamid et al., 2009; Al-Qahtani et al., 2010; Janecke et al., 2002; Marlin et al., 2001); Observed in unaffected parents of children with hearing loss who were heterozygous for the variant in published literature (Bonyadi et al., 2009; Leone et al., 2017); Published functional studies demonstrate a damaging effect on gap junction function (Press et al., 2017; Bruzzone et al., 2003); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25388846, 19941053, 12505163, 20086291, 24529908, 22208444, 24158611, 11493200, 12189487, 28428247, 21996152, 14643477, 26096904, 21388256, 22695344, 28263784, 19929407, 15964725, 30989077, 19715472, 20086306, 16380907, 17041943, 12872268, 31620696, 34426522, 34335733, Chaleshtori2005[article], 33096615, 31569309, 21281533, 31412945) -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 30, 2022	The p.Met163Val variant in GJB2 has been identified in >10 probands with non-syndromic hearing loss from several ethnic populations; however, a pathogenic variant on the second allele of GJB2 was not detected in any of these probands (Al-Qahtani 2010, Amorini 2015, Bayazit 2003, Bonyadi 2009, Bonyadi 2014, Chaleshtori 2002, Chaleshtori 2005, Dalamon 2005, Falah 2012, Gunther 2003, Janecke 2002, Mahdieh 2011, Marlin 2001, Padma 2009, Tang 2006, Yilmaz 2010). In two families with post-lingual progressive hearing loss described in one study, two parent-to-child segregations were reported for this variant suggesting that the variant may lead to autosomal dominant hearing loss (Falah 2012). However, the majority of probands in the other studies did not report autosomal dominant inheritance of hearing loss. Two other missense variants at the same amino acid position (p.Met163Leu and p.Met163Thr) have also been reported in individuals with hearing loss, and in vitro functional studies of the p.Met163Val and p.Met163Leu show an impact to the normal activity of the protein due to these variants (Bruzzone 2003, Matos 2008). This data suggests that variants at this amino acid position are not tolerated. The p.Met163Val variant has also been identified 10/16478 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs80338949); however this frequency is not high enough to rule out pathogenicity. In summary, the presence of the p.Met163Val variant in several affected individuals and the functional data suggests a pathogenic role for the variant, however the clinical significance of this variant cannot be determined with certainty given the absence of a second pathogenic variant in heterozygous probands and limited segregation data. ACMG/AMP Criteria applied:BS1, PP3. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Sep 26, 2022	This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 163 of the GJB2 protein (p.Met163Val). This variant is present in population databases (rs80338949, gnomAD 0.07%). This missense change has been observed in individual(s) with deafness (PMID: 11493200, 12189487, 21281533, 22208444, 26096904). ClinVar contains an entry for this variant (Variation ID: 21388). 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) has been performed at Invitae 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 have shown that this missense change affects GJB2 function (PMID: 12505163, 28428247). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 07, 2021	- -

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

not provided, no classification provided	literature only	GeneReviews	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Mar 01, 2023	The missense c.487A>G(p.Met163Val) variant in GJB2 gene has been reported previously in heterozygous state in multiple individuals affected with GJB2-related hearing loss (Smith et. al., 2016; Günther et. al., 2003). This variant has been observed to segregate with disease in related individuals (Falah et. al., 2012). Functional studies demonstrate a damaging effect on gap junction function, impacting GJB2 function (Press ER, et. al., 2017; Bruzzone R, et. al.,2003). The p.Met163Val variant has been reported with allele frequency of 0.01% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Uncertain Significance / Likely Pathogenic. The amino acid change p.Met163Val in GJB2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Met at position 163 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

Hearing impairment Pathogenic:1

Likely pathogenic, flagged submission

clinical testing

Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center

Apr 12, 2021

PS1_Strong, PM2_Moderate, PM5_Moderate, PP3_Supporting -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Dec 24, 2021

Variant summary: GJB2 c.487A>G (p.Met163Val) results in a conservative amino acid change located in the extracellular 2 domain (Tang_2006) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 251140 control chromosomes, predominantly at a frequency of 0.00075 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 2.2 fold of the estimated maximal expected allele frequency for a pathogenic variant in GJB2 causing Non-Syndromic Hearing Loss phenotype (0.00034), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. c.487A>G has been reported in the literature as a VUS with a non-informative genotype (i.e., second allele not specified or heterozygous) for a recessive mode of inheritance among individuals with various forms of moderate non sensorineural hearing loss undergoing genetic evaluation in small and large sized gene panels for hearing loss (example, Marlin_2001, Janecke_2002, Bayazit_2003, Tang_2006, Hamid_2009, Padma_2009, Bonyadi_2009, Yilmaz_2010, Al-Qahtani_2010, Mahdieh_2011, Falah_2012, Leone_2017, Buonfiglio_2020, Xie_2021). At-least one individual with moderate hearing loss reported a homozygous genotype although no family history, co-segregation/co-occurrence was specified (Amorini_2015). One family where the variant was transmitted from a father with late onset hearing impairment to two affected siblings with early onset hearing loss reported a possible instance of autosomal dominant transmission with anticipation (Falah_2012). Another report speculates a role in digenic inheritance with synergistic heterozygosity for this variant and variants in the TMPRSS3 gene (Leone_2017). However, a firm conclusion regarding these atypical modes of inheritance remain speculative. These data indicate that the variant may be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function (example, Bruzzone_2003, Press_2017). The most pronounced variant effect results in a complete inability to form homotypic channels since the level of junctional conductance measured never exceeded background values (Bruzzone_2003) and impaired gap junction function (Press_2017). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with a predominant consensus as VUS (n=6) (likely pathogenic, n=1). Some submitters cite overlapping evidence utilized in the context of this evaluation and the prevailing interpretation even in most recent publications remains as VUS (example, Buonfiglio_2020). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Nonsyndromic genetic hearing loss Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

INGEBI, INGEBI / CONICET

Aug 31, 2020

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of c.487A>G, p.Met163Val variant in GJB2 gene is 0,05% (23/30604 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 rule. Computational evidence predicted a pathogenic effect of the mutation to the protein (REVELscore: 0.869) applying to PP3 criteria. The p.Met163Val change has been identified only in heterozygous state in several patients (PMID: 11493200, 14643477, 15964725, 12189487, 12872268). Besides, in two familial cases this variant segregate in two affected individuals and their affected fathers (PMID:22208444). So, this evidence is not enough to be counted. On the other hand, p.Met163Val change was identified in homozygous state in a control subject meeting BS2 rule (PMID: 20086291). Functional studies demonstrated a highly reduction of dye transfer of p.Met163Val mutant in HeLa cells (PMID:28428247). Besides, it was shown that this mutant was unable to form functional gap junction channels in Xenopus Laevis oocytes (PMID:12505163). Hence, PS3_Moderate criteria was applied. In summary, the clinical significance of this variant is currently uncertain (PM2_Supporting, PP3, PS3_Moderate, BS2). -

Autosomal dominant nonsyndromic hearing loss 3A Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Pathogenic	0.38
Cadd	Uncertain	24
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.70	D;D;D
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Uncertain	0.14	D
MetaRNN	Benign	0.22	T;T;T
MetaSVM	Uncertain	0.76	D
MutationAssessor	Benign	1.2	L;L;L
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-2.2	N;N;.
REVEL	Pathogenic	0.87
Sift	Benign	0.23	T;T;.
Sift4G	Benign	0.17	T;T;.
Polyphen		0.91	P;P;P
Vest4		0.93
MVP		0.90
MPC		0.082
ClinPred		0.22	T
GERP RS		5.5
Varity_R		0.67
gMVP		0.89

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: rs80338949; hg19: chr13-20763234;