13-20189031-C-T

Position:

• chr13-20189031-C-T

Variant summary

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

The ENST00000382848.5(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 ENST00000382848.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:17 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 hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in ENST00000382848.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-20189032-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 560669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• 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/exons	MANE	Protein	UniProt
GJB2	NM_004004.6	c.551G>A	p.Arg184Gln	missense_variant	2/2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.551G>A	p.Arg184Gln	missense_variant	2/2		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.551G>A	p.Arg184Gln	missense_variant	2/2	1	NM_004004.6	ENSP00000372299	P1
GJB2	ENST00000382844.2	c.551G>A	p.Arg184Gln	missense_variant	1/1			ENSP00000372295	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:17 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 07, 2023	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Jan 14, 2016	- -
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	Athena Diagnostics	Jun 02, 2022	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). -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Feb 01, 2021	- -

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

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2010	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	Dec 07, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	May 09, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 20, 2017	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

Pathogenic, no assertion criteria provided	clinical testing	Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals	Mar 31, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 24, 2022	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

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

May 28, 2019

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

Pathogenic, no assertion criteria provided

clinical testing

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

Apr 07, 2014

- -

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Integrating Genomics into Medicine, Frazer Institute, University Of Queensland

Jun 02, 2023

- -

Hearing impairment Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Feb 08, 2013

- -

Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 28, 2018

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
MutationTaster	Benign	1.0	D;D
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;