13-20189031-C-T

Variant names:

• chr13-20189031-C-T
• rs80338950
• NM_004004.6:c.551G>A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_004004.6(GJB2):​c.551G>A​(p.Arg184Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R184P) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:18 O:1
• Conservation: PhyloP100: 7.86

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 18 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
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-20189031-C-G is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.988
• PP5: Variant 13-20189031-C-T is Pathogenic according to our data. Variant chr13-20189031-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 29662.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20189031-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJB2	NM_004004.6	c.551G>A	p.Arg184Gln	missense_variant	Exon 2 of 2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.551G>A	p.Arg184Gln	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.551G>A	p.Arg184Gln	missense_variant	Exon 2 of 2	1	NM_004004.6	ENSP00000372299.4
GJB2	ENST00000382844.2	c.551G>A	p.Arg184Gln	missense_variant	Exon 1 of 1	6		ENSP00000372295.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:18 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:7

Jan 14, 2016

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2021

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 07, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a dominant negative effect of the resulting connexin-26 protein on the wild-type connexin 26 and connexin 30 proteins (Yum et al., 2010; Zhang et al., 2011); Not observed in large population cohorts (gnomAD); 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: 29921236, 20442751, 21868108, 21040787, 20096356, 25388846, 20937258, 12111646, 11439000, 31827275, 32645618, 34599368, 24945352) -

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 02, 2022

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant segregates in multiple families with dominant nonsyndromic hearing loss and has been confirmed to occur de novo in individuals. This variant has also been reported heterozygous in at least one individual with syndromic hearing loss. At least one other missense variant at this codon is considered to be pathogenic or likely pathogenic, suggesting this variant may also cause disease. Computational tools yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites. Assessment of experimental evidence suggests this variant results in abnormal protein function. Studies showed this variant impaired gap junction channels and demonstrated a dominant-negative effect (PMID: 20096356, 21040787). -

Jun 07, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 184 of the GJB2 protein (p.Arg184Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant non-syndromic deafness (PMID: 11439000, 35301649). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 29662). 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%. For these reasons, this variant has been classified as Pathogenic. -

Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:4 Other:1

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Sep 01, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Dec 07, 2018

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 09, 2017

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 20, 2017

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

A heterozygous missense variant was identified, NM_004004.5(GJB2):c.551G>A in exon 2 of the GJB2 gene.This substitution creates a minor amino acid change from an arginine to a glutamine at position 184, NP_003995.2(GJB2):p.(Arg184Gln). The argine at this position has very high conservation (100 vertebrates, UCSC). In silico tools predict this variant to be deleterious (Polyphen, SIFT, CADD, Mutation Taster).This variant is not present in the gnomAD population database. It has been previously reported as a dominant pathogenic variant in patients with nonsyndromic hearing loss (Huang. et al., (2011), Wang et al., (2002), Pang et al., (2014), Hamelmann et al., (2001)).It is not situated in a known functional domain. In addition, functional studies show that this variant causes mislocalisation of the GJB2 protien and results in a dominant negative disease mechanism (Su et al., (2010)). Based on current information, this variant has been classified as LIKELY PATHOGENIC. -

Nonsyndromic genetic hearing loss Pathogenic:2

Mar 31, 2023

Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 24, 2022

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GJB2 c.551G>A (p.Arg184Gln) results in a 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 was absent in 254160 control chromosomes (gnomAD). c.551G>A has been reported in the literature in multiple individuals affected with Autosomal Dominant Non-Syndromic Hearing Loss and the variant segregated with the disease (examples: Hamelmann_2001, Hwa_2003, Putcha_2007, Su_2010 and delaLuzArenas-Sordo_2012). The variant has also been identified in multiple individuals as a de novo occurrence (examples: Huang_2011 and Mahdieh_2010). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function showed a dominant negative effect on both connexin 26 and connexin 30 (example: Su 2010). Nine submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all laboratories classified the variant as pathogenic (n=8) and likely pathogenic(n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

not specified Pathogenic:1

May 28, 2019

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The GJB2 c.551G>A; p.Arg184Gln variant (rs80338950) is reported in the literature in multiple individuals affected with autosomal dominant nonsyndromic hearing loss (Amritkumar 2018, Hamelmann 2001, Wang 2002), including several confirmed de novo cases (Huang 2011, Pang 2014). Functional analyses of the variant protein show a dominant negative effect on both connexin 26 and connexin 30 in vitro (Su 2010, Yum 2010, Zhang 2011). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 29662), and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 184 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Based on available information, this variant is considered to be pathogenic. References: Amritkumar P et al. Role of DFNB1 mutations in hereditary hearing loss among assortative mating hearing impaired families from South India. BMC Med Genet. 2018 Jun 19;19(1):105. Hamelmann C Pattern of connexin 26 (GJB2) mutations causing sensorineural hearing impairment in Ghana. Hum Mutat. 2001;18(1):84-5. Huang S et al. De novo dominant mutation of GJB2 in two Chinese families with nonsyndromic hearing loss. Int J Pediatr Otorhinolaryngol. 2011 Oct;75(10):1333-6. Pang X et al. Characterization of spectrum, de novo rate and genotype-phenotype correlation of dominant GJB2 mutations in Chinese hans. PLoS One. 2014 Jun 19;9(6):e100483. Su CC et al. Mutation R184Q of connexin 26 in hearing loss patients has a dominant-negative effect on connexin 26 and connexin 30. Eur J Hum Genet. 2010 Sep;18(9):1061-4. Wang YC et al. Mutations of Cx26 gene (GJB2) for prelingual deafness in Taiwan. Eur J Hum Genet. 2002 Aug;10(8):495-8. Yum SW et al. Dominant connexin26 mutants associated with human hearing loss have trans-dominant effects on connexin30. Neurobiol Dis. 2010 May;38(2):226-36. Zhang J et al. Dominant Cx26 mutants associated with hearing loss have dominant-negative effects on wild type Cx26. Mol Cell Neurosci. 2011 Jun;47(2):71-8. -

Hearing loss Pathogenic:1

Apr 07, 2014

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

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:1

Jun 02, 2023

Integrating Genomics into Medicine, Frazer Institute, University Of Queensland

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hearing impairment Pathogenic:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Rare genetic deafness Pathogenic:1

Nov 28, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Arg184Gln variant in GJB2 has been reported in >10 individuals with hearin g loss (Amritkumar 2018, de la luz Arenas-Sordo, Hamelmann 2001, Huang 2011, Mad ieh 2010, Minarik 2012, Pang 2014, Weegerink 2011). It has been identified as a de novo variant in 5 of these individuals (Huang 2011, Madieh 2010, Pang 2014). The variant segregated in a total of 7 affected family members, with two familie s displaying autosomal dominant inheritance (Hamelmann 2001, Pavithra 2017, Weeg erink). The third family had additional GJB2 variants (Gln124X and IVS1+1G>A) th at also segregated with p.Arg184Gln in the affected family members (Pavithra 201 7, Amritkumar 2018). This variant was absent from large population studies. In v itro functional studies also suggest that this variant colocalize and coimmunopr ecipitate with wild-type Cx26 and Cx30 and inhibits dye transfer (Yum 2010, Zhan g 2011). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hearing loss. ACMG/AMP criteria applied: PS2_VeryStrong, PP1_Strong, PM2, PS4_Moderate, PP3, PS3_Supporting. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.95	D;D;D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.97
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.98	.;.;D
M_CAP	Pathogenic	0.49	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.6	H;H;H
PrimateAI	Uncertain	0.67	T
PROVEAN	Uncertain	-3.4	D;D;.
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0010	D;D;.
Sift4G	Pathogenic	0.0010	D;D;.
Polyphen		1.0	D;D;D
Vest4		0.97
MutPred		0.91		Gain of ubiquitination at K188 (P = 0.0719);Gain of ubiquitination at K188 (P = 0.0719);Gain of ubiquitination at K188 (P = 0.0719);
MVP		0.97
MPC		0.30
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.92
gMVP		0.96

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: rs80338950; hg19: chr13-20763170; COSMIC: COSV67010732;