rs104894402

chr13-20189359-G-Achr13-20189359-G-C

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.223C>T(p.Arg75Trp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging 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. R75G) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 3.75

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 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 6 uncertain 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 chr13-20189358-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 17027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 13-20189359-G-A is Pathogenic according to our data. Variant chr13-20189359-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 17011.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20189359-G-A is described in Lovd as [Pathogenic]. Variant chr13-20189359-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.223C>T	p.Arg75Trp	missense_variant	2/2	ENST00000382848.5
GJB2	XM_011535049.3	c.223C>T	p.Arg75Trp	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.223C>T	p.Arg75Trp	missense_variant	2/2	1	NM_004004.6	P1
GJB2	ENST00000382844.2	c.223C>T	p.Arg75Trp	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 18, 2022	Published functional studies demonstrate a damaging effect (exerts a dominant negative effect on co-expressed wildtype protein, alters Cx26 channel activity, and delays apoptosis) (Rouan et al., 2001; Zhang et al., 2011; Inoshita et al., 2014); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20890442, 17462767, 9856479, 12384501, 25388846, 12668604, 12064628, 18924167, 14681039, 18941476, 16009703, 11493646, 21040787, 20096356, 26763877, 21510145, 18793701, 17666888, 16945493, 12700168, 20301708, 34440452, 30168495, 33096615, 20583176, 24945352, 11354642, 24387126) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 07, 2019	The GJB2 c.223C>T; p.Arg75Trp variant (rs104894402) is reported in the literature in multiple individuals and families affected with either syndromic or nonsyndromic autosomal dominant hearing loss (ADHL), including some individuals with palmoplantar keratoderma (Lee 2010, Pang 2014, Richard 1998, Weegerink 2011, Yuan 2009). This variant is reported in ClinVar (Variation ID: 17011), and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. Additionally, another variant at this codon (c.224G>A; p.Arg75Gln) has been reported in individuals with ADHL and is considered pathogenic (Pang 2014). The arginine at codon 75 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Functional analyses of the variant protein show that arginine 75 is critical to the formation of gap junctions, and variants at this codon have dominant negative effects (Deng 2006, Marziano 2003, Richard 1998, Zhang 2011). Based on available information, the p.Arg75Trp variant is considered to be pathogenic. References: Deng Y et al. Mutations of connexin 26 at position 75 and dominant deafness: essential role of arginine for the generation of functional gap-junctional channels. Hear Res. 2006 Oct;220(1-2):87-94. Lee JY et al. Hereditary palmoplantar keratoderma and deafness resulting from genetic mutation of Connexin 26. J Korean Med Sci. 2010 Oct;25(10):1539-42. Marziano NK et al. Mutations in the gene for connexin 26 (GJB2) that cause hearing loss have a dominant negative effect on connexin 30. Hum Mol Genet. 2003 Apr 15;12(8):805-12. 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. Richard G et al. Functional defects of Cx26 resulting from a heterozygous missense mutation in a family with dominant deaf-mutism and palmoplantar keratoderma. Hum Genet. 1998 Oct;103(4):393-9. Weegerink NJ Phenotypes of two Dutch DFNA3 families with mutations in GJB2. Ann Otol Rhinol Laryngol. 2011 Mar;120(3):191-7. Yuan Y et al. A de novo GJB2 (connexin 26) mutation, R75W, in a Chinese pedigree with hearing loss and palmoplantar keratoderma. Am J Med Genet A. 2009 Feb 15;149A(4):689-92. 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. -

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

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 2003	- -

Palmoplantar keratoderma-deafness syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center of Genomic medicine, Geneva, University Hospital of Geneva

Apr 22, 2020

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Hereditary palmoplantar keratoderma;C5680182: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 c.223C>T, p.Arg75Trp is absent from population databases (gnomAD, GO-ESP, 1000 genomes) meeting PM2 criteria. It was found in 1/154 Egyptian controls who did not show skin disease but they had not been tested for hearing loss (PMID: 9856479) so that this evidence was not counted. The novo confirmed occurrences have been detected in two sporadic non-syndromic hearing loss cases (PMID: 11354642, 2151045) and three syndromic cases (hearing loss and palmoplantar keratoderma; PMID: 18924167, 24945352), meeting PS2_VeryStrong criteria. The p.Arg75Trp change has segregated in three different families with palmoplantar keratoderma and hearing impairment (PMID: 9856479, 20890442, 24945352) applying to PP1_Supporting rule. Besides, this variant was detected in heterozygous state in several sporadic non-syndromic hearing loss patients (PMID: 10980526, 17666888, 18941476) meeting PS4_Moderate criteria. Computational evidence predicted that the mutation has a damaging impact to the protein (REVEL=0.97; PP3). Functional studies in HeLa cells (dye transfer assays) demonstrated a dominant effect of p.Arg75Trp mutant when it was co-injected with CX26WT and CX30WT (completely inhibition of dye transfer); PMID: 12668604, 18941476. In addition to this, functional studies also showed that p.Arg75Trp mutant was incapable of inducing electrical conductance between adjacent cells and it almost completely suppressed the activity of co-expressed WT protein in Xenopus laevis oocytes (PMID: 9856479). Furthermore, transgenic mice expressing R75WCX26 mutant showed severe-profound hearing loss, deformity of supporting cells failure in the formation of the tunnel of Corti and degeneration of sensory hair cells (PMID:12700168) and it was demonstrated its importance for the postnatal development of the organ of Corti and normal hearing (PMID:18793701). Therefore, the c.223C>T variant meets criteria to be classified as pathogenic for autosomal dominant non-syndromic hearing loss and syndromic hearing loss (palmoplantar keratoderma and deafness) (PM2, PS2_VeryStrong, PS4_Moderate, PP1_Supporting, PP3 and PS3_Strong). -

Hearing loss, autosomal recessive Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

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Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Sep 29, 2014

The p.Arg75Trp variant in GJB2 has been identified as the only GJB2 variant in a t least 11 individuals with hearing loss and was not identified in 120 Indian co ntrol chromosomes and 802 Chinese control chromosomes (Richard 1998, Putcha 2007 , Mani 2009, Yuan 2009, Lee 2010, Weegerink 2011, Pang 2014 and LMM unpublished data). Most reported individuals had severe to profound hearing loss that was ei ther congenital or progressive in infancy and some individuals also had palmopla ntar keratoderma. This variant occurred de novo in 3 individuals and was identif ied in three affected parents, which supports that this variant is inherited in a dominant manner (Richard 1998, Yuan 2009, Lee 2010, Weegerink 2011, Pang 2014) . This variant has not been identified in large population studies. Furthermore, Arginine at position 75 is highly conserved across species and other analogous connexin proteins (Deng, 2006). The functional assay demonstrated that the chan ge to a Tryptophan (Trp) at position 75 has a dominant negative affect on the pr otein and disrupts the function of the gap junction (Richard 1998, Maziano 2003, Deng 2006, Zhang 2011) and is important for the postnatal development of the or gan of Corti and normal hearing (Inoshita 2008, Inoshita 2014). In summary, this variant meets our criteria to be classified as pathogenic (http://pcpgm.partner s.org/LMM). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
Cadd	Pathogenic	31
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.95	D;D;D
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Uncertain	0.92	D
M_CAP	Pathogenic	0.56	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.7	H;H;H
MutationTaster	Benign	1.0	A;A
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-8.0	D;D;.
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D;D;.
Sift4G	Pathogenic	0.0	D;D;.
Polyphen		1.0	D;D;D
Vest4		0.96
MutPred		0.98		Gain of helix (P = 0.132);Gain of helix (P = 0.132);Gain of helix (P = 0.132);
MVP		0.98
MPC		0.29
ClinPred		1.0	D
GERP RS		5.2
Varity_R		0.98
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: rs104894402; hg19: chr13-20763498;