13-20189155-G-A

Position:

• chr13-20189155-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM5 PP3_Moderate PP5_Very_Strong

The NM_004004.6(GJB2):​c.427C>T​(p.Arg143Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R143L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00020 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000094 (0 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:23 O:1
• Conservation: PhyloP100: 0.707

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 14 ACMG points.

• PM1: In a chain Gap junction beta-2 protein (size 225) in uniprot entity CXB2_HUMAN there are 70 pathogenic changes around while only 16 benign (81%) in NM_004004.6
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-20189154-C-A is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.854
• PP5: Variant 13-20189155-G-A is Pathogenic according to our data. Variant chr13-20189155-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 17009.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20189155-G-A is described in Lovd as [Pathogenic]. Variant chr13-20189155-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GJB2	NM_004004.6	c.427C>T	p.Arg143Trp	missense_variant	2/2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.427C>T	p.Arg143Trp	missense_variant	2/2		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.427C>T	p.Arg143Trp	missense_variant	2/2	1	NM_004004.6	ENSP00000372299	P1
GJB2	ENST00000382844.2	c.427C>T	p.Arg143Trp	missense_variant	1/1			ENSP00000372295	P1

Frequencies

GnomAD3 genomes AF: 0.000197 AC: 30 AN: 152180 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000531

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000116 AC: 29 AN: 250932 Hom.: 0 AF XY: 0.0000958 AC XY: 13 AN XY: 135706

Gnomad AFR exome AF: 0.000740

Gnomad AMR exome AF: 0.0000868

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000109

Gnomad SAS exome AF: 0.0000980

Gnomad FIN exome AF: 0.000139

Gnomad NFE exome AF: 0.0000529

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000937 AC: 137 AN: 1461790 Hom.: 0 Cov.: 33 AF XY: 0.0000839 AC XY: 61 AN XY: 727178

Gnomad4 AFR exome AF: 0.00137

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000655

Gnomad4 SAS exome AF: 0.0000348

Gnomad4 FIN exome AF: 0.000244

Gnomad4 NFE exome AF: 0.0000315

Gnomad4 OTH exome AF: 0.0000993

GnomAD4 genome AF: 0.000197 AC: 30 AN: 152298 Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14 AN XY: 74470

Gnomad4 AFR AF: 0.000529

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000588

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.0000617 Hom.: 0

Bravo AF: 0.000249

ESP6500AA AF: 0.000681 AC: 3

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000165 AC: 20

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:23 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 15, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 08, 2021	The GJB2 c.427C>T; p.Arg143Trp variant (rs80338948) is a well-studied pathogenic variant associated with autosomal recessive deafness-1A (DFNB1A) and has been observed in affected individuals both in the homozygous state and in trans to other pathogenic GJB2 variants (Abe 2018, Brobby 1998, Dodson 2011, Sloan-Heggen 2016). This variant is found in the African population with an overall allele frequency of 0.07% (18/24908 alleles) in the Genome Aggregation Database, and it is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 17009). The arginine at codon 143 is highly conserved, and while conclusions from functional studies are somewhat varied, functional assays indicate that the p.Arg143Trp variant inhibits gap junction formation and reduced conductance (Wang 2003, Mese 2004, Palmada 2006). Additionally, other amino acid substitutions at this codon (p.Arg143Gln, p.Arg143Leu) have been reported in individuals with hearing loss and are considered disease-causing (Loffler 2001, Putcha 2007). Based on available information, the p.Arg143Trp variant is considered to be pathogenic. References: Abe S et al. Diagnostic pitfalls for GJB2-related hearing loss: A novel deletion detected by Array-CGH analysis in a Japanese patient with congenital profound hearing loss. Clin Case Rep. 2018 Sep 21;6(11):2111-2116. Brobby et al. Connexin 26 R143W mutation associated with recessive nonsyndromic sensorineural deafness in Africa. N Engl J Med. 1998; 338(8): 548-550. Dodson et al. Vestibular dysfunction in DFNB1 deafness. Am J Med Genet A. 2011; 155A(5): 993-1000. Loffler J et al. Sensorineural hearing loss and the incidence of Cx26 mutations in Austria. Eur J Hum Genet. 2001 Mar;9(3):226-30. Mese et al. Altered gating properties of functional Cx26 mutants associated with recessive non-syndromic hearing loss. Hum Genet. 2004; 115(3): 191-199. Palmada et al. Loss of function mutations of the GJB2 gene detected in patients with DFNB1-associated hearing impairment. Neurobiol Dis. 2006; 22(1): 112-118. 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. Sloan-Heggen et al. Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet. 2016; 135(4): 441-450. Wang et al. Functional analysis of connexin-26 mutants associated with hereditary recessive deafness. J Neurochem. 2003; 84(4): 735-742. -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2024	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 16300957, 25388846, 30455902, 34943631, 25087612, 12833397, 21465647, 25266519, 15241677, 12562518, 19043807, 31370293, 31162818, 30146550, 32012697, 9393973, 15235031, 31541171, 31160754, 30275481, 32645618, 33597575, 33096615, 31589614, 29871260, 33297549, 32067424, 36147510, 34599368, 35114279, 35939872, 37108562, 35336849, 36493725, 35982127, 9471561, 38069086, 34519870, 37561809, 36048236, 35853923) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 28, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 01, 2019	The best available variant frequency is uninformative because it is below the disease allele frequency. Statistically enriched in patients compared to ethnically matched controls. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Occurs in three or more cases with a recessive pathogenic variant in the same gene. Damaging to protein function(s) relevant to disease mechanism. Very strong co-segregation with disease, and data include affected and unaffected individuals from multiple families. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 143 of the GJB2 protein (p.Arg143Trp). This variant is present in population databases (rs80338948, gnomAD 0.07%). This missense change has been observed in individuals with hearing loss (PMID: 15365987, 15617546, 18941476, 19715472, 23638949, 26061264, 27792752). ClinVar contains an entry for this variant (Variation ID: 17009). 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 with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GJB2 function (PMID: 9393973, 15235031). For these reasons, this variant has been classified as Pathogenic. -

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:7 Other:1

Likely pathogenic, no assertion criteria provided	case-control	Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital	Feb 26, 2019	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 01, 2002	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Mar 05, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	May 09, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 21, 2016	Variant summary: The c.427C>T variant affects a non-conserved nucleotide, resulting in amino acid change from Arg to Trp. 5/5 in-silico tools predict damaging outcome for this variant. This variant is found in 20/121442 control chromosomes at a frequency of 0.0001647, which does not exceed maximal expected frequency of a pathogenic allele (0.025). The variant of interest has been reported to be a common pathogenic variant predominantly found in Ghana (Hamelmann_2001). In addition, multiple clinical laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 24, 2019	NM_004004.5(GJB2):c.427C>T(R143W) is classified as pathogenic in the context of GJB2-related DFNB1 nonsyndromic hearing loss and deafness. Sources cited for classification include the following: PMID 11439000, 12562518, 15241677 and 16300957. Classification of NM_004004.5(GJB2):c.427C>T(R143W) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.‚Äã -

Hearing loss Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

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

Oct 02, 2014

- -

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Dec 10, 2021

GJB2 NM_004004.5 exon 2 p.Arg143Trp (c.427C>T): This variant has been reported in the literature in the homozygous or compound heterozygous state in several individuals with nonsyndromic hearing loss, segregating with disease in multiple affected family members (Brobby 1998 PMID:9471561, Abe 2000 PMID:10633133, Maheshwari 2003 PMID:12833397, Cryns 2004 PMID:14985372, Kenna 2010 PMID:20083784, Dodson 2011 PMID:21465647, Abe 2018 PMID:30455902). This variant is present in 0.07% (18/24908) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/13-20763294-G-A). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, carrier status, and/or variable expressivity. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:17009). Evolutionary conservation and computational predictive tools support that this variant may impact the protein. In addition, functional studies have shown that this mutant protein is unable to from functional channels (Palmada 2006 PMID:16300957). However, these studies may not accurately represent in vivo biological function. In summary, this variant is classified as pathogenic based on the data above (segregation studies, impact to protein etc.). -

Nonsyndromic genetic hearing loss Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

INGEBI, INGEBI / CONICET

Aug 21, 2020

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of the c.427C>T, p.Arg143Trp variant in GBJ2 gene is 0,04% (18/24908 African chromosomes 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 PM2_Supporting criteria. The p.Arg143Trp change was identified in trans with at least 7 known pathogenic variants applying to PM3_VeryStrong rule(PMID: 9471561, 14985372, 10633133, 11556849, 10982180, 24158611). In one family this variant was identified in trans with a reported pathogenic variant and segregated among family members applying to PP1_Supporting criteria (PMID: 10633133). Computational analysis predicted a pathogenic impact of the mutation to the protein (REVEL=0.918; PP3). Functional studies demonstrated that p.Arg143Trp mutant formed functional channels that were permeable to fluorescent tracers in transfected N2A cells and conductance levels measured similar to that of WT-Cx26 (PMID: 12562518). However, it did not induce the formation of functional GJCh in paired Xenopus laevis oocytes (PMID: 15241677, 16300957). As the evidence is contradictory functional data was not counted. In summary, This variant meets criteria to be classified as pathogenic for autosomal recessive non-syndromic hearing loss: PM2_Supporting, PM3_VeryStrong, PP1_Supporting and PP3. -

Hearing impairment Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Feb 08, 2013

- -

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1844678:X-linked mixed hearing loss with perilymphatic gusher;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 03, 2021

- -

GJB2-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 30, 2024

The GJB2 c.427C>T variant is predicted to result in the amino acid substitution p.Arg143Trp. This variant was reported in an individual with autosomal recessive nonsyndromic hearing loss (Brobby et al 1998. PubMed ID: 9471561; Maheshwari et al. 2003. PubMed ID: 12833397; Abe et al. 2018. PubMed ID: 30455902). This variant is reported in 0.072% of alleles in individuals of African descent in gnomAD. This variant is interpreted as pathogenic. -

Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2016

This variant was classified as: Pathogenic. -

Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

May 14, 2019

The p.Arg143Trp variant in GJB2 has been reported in many probands with hearing loss (Brobby 1998, Abe 2000, Rabionet 2000, Kenna 2001, Cryns 2004, Chaleshtori 2005, Snoeckx 2005, LMM data). Most of these probands were homozygous or compound heterozygous. It has also been identified in 0.07% (18/24908) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org); however, this frequency is low enough to be consistent with a recessive carrier frequency for autosomal recessive nonsyndromic hearing loss. Computational prediction tools and conservation analysis suggest that this variant may impact the protein. Furthermore, in vitro functional studies support an impact on protein function (Meşe 2004, Palmada 2006). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive hearing loss. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3_Supporting, PP3. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.95	D;D;D
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Uncertain	0.94	.;.;D
M_CAP	Pathogenic	0.33	D
MetaRNN	Pathogenic	0.85	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.6	M;M;M
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.59	T
PROVEAN	Pathogenic	-6.3	D;D;.
REVEL	Pathogenic	0.92
Sift	Pathogenic	0.0	D;D;.
Sift4G	Pathogenic	0.0	D;D;.
Polyphen		1.0	D;D;D
Vest4		0.86
MVP		0.98
MPC		0.29
ClinPred		0.53	D
GERP RS		4.6
Varity_R		0.89
gMVP		0.98

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: rs80338948; hg19: chr13-20763294;