chr13-20189325-G-C

Position:

• chr13-20189325-G-C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PP3_Strong PP5_Very_Strong

The NM_004004.6(GJB2):​c.257C>G​(p.Thr86Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,778 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 Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 8.06

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 helix (size 29) in uniprot entity CXB2_HUMAN there are 23 pathogenic changes around while only 1 benign (96%) in NM_004004.6
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.994
• PP5: Variant 13-20189325-G-C is Pathogenic according to our data. Variant chr13-20189325-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 631697.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GJB2	NM_004004.6	c.257C>G	p.Thr86Arg	missense_variant	2/2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.257C>G	p.Thr86Arg	missense_variant	2/2		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.257C>G	p.Thr86Arg	missense_variant	2/2	1	NM_004004.6	ENSP00000372299.4
GJB2	ENST00000382844.2	c.257C>G	p.Thr86Arg	missense_variant	1/1	6		ENSP00000372295.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251278 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135812

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000753 AC: 11 AN: 1461778 Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7 AN XY: 727200

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000277

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 15, 2018	Across a selection of the available literature, the GJB2 c.257C>G (p.Thr86Arg) missense variant, which has been found mainly in the East Asian population, was identified in a homozygous state in at least one individual with autosomal recessive nonsyndromic hearing loss and in a compound heterozygous state in at least four unrelated individuals, also with autosomal recessive nonsyndromic hearing loss (Ohtsuka et al. 2003; Choi et al. 2009; Shi et al. 2016; Sakuma et al. 2016; Zhang et al. 2016). Huang et al. (2013) further identified one patient with profound bilateral sensorineural hearing loss and enlarged vestibular aqueduct with double biallelic variants in the GJB2 and SLC26A4 genes; the patient was compound heterozygous for the p.Thr86Arg variant and a pathogenic frameshift variant common in the East Asian population. The p.Thr86Arg variant was absent from 247 controls but is reported at a frequency of 0.00006 in the East Asian population of the Genome Aggregation Database, based on one allele in a region of good sequence coverage so the variant is presumed to be rare. HEK293 cells transfected with the variant protein demonstrated that the p.Thr86Arg variant led to defective intercellular trafficking and oligomerization of the protein (Choi et al. 2009). Co-transfection with the wild type channel demonstrated that the p.Thr86Arg variant did not affect ionic transfer and biochemical coupling, consistent with the recessive nature of the variant. Based on the collective evidence, the p.Thr86Arg variant is classified as pathogenic for autosomal recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Juno Genomics, Hangzhou Juno Genomics, Inc	-	PM2_Supporting+PM3_VeryStrong+PS3_Moderate -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 28, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 07, 2024	This sequence change replaces threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 86 of the GJB2 protein (p.Thr86Arg). This variant is present in population databases (no rsID available, gnomAD 0.006%). This missense change has been observed in individuals with autosomal recessive deafness (PMID: 19384972, 26763877, 30896630, 31160754). ClinVar contains an entry for this variant (Variation ID: 631697). 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: 19384972). For these reasons, this variant has been classified as Pathogenic. -

nonsyndromic sensorineural hearing loss Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

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

Oct 02, 2020

- -

Nonsyndromic genetic hearing loss Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Jun 20, 2023

Variant summary: GJB2 c.257C>G (p.Thr86Arg) results in a non-conservative amino acid change located in the Connexin, N-terminal domain (IPR013092) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251278 control chromosomes (gnomAD). c.257C>G has been reported in the literature as a biallelic genotype in multiple individuals affected with Hearing Loss (e.g. Ohtsuka_2003, Choi_2009, Huang_2013, Xu_2014). These data indicate that the variant is very likely to be associated with disease. When expressed alone in HEK293 cells, the variant protein failed to form gap junctions and had deficient hemichannel opening (Choi_2009). This deficiency was rescued when the variant was co-expressed with WT-GJB2, supporting the recessive nature of this specific variant. The following publications have been ascertained in the context of this evaluation (PMID: 19384972, 23266159, 12560944, 24941117). Six ClinVar submitters have assessed this variant since 2014: one classified the variant as uncertain significance, one as likely pathogenic, and four as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

3billion

Jan 03, 2022

Same nucleotide change resulting in same amino acid change has been previously reported to be associated with GJB2 related disorder (PMID:12560944, PS1_P). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PM3_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.969, 3CNET: 0.989, PP3_P). A missense variant is a common mechanism associated with Deafness (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2_M). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D;D;D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	.;.;D
M_CAP	Pathogenic	0.58	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.5	M;M;M
PrimateAI	Uncertain	0.78	T
PROVEAN	Uncertain	-4.3	D;D;.
REVEL	Pathogenic	0.97
Sift	Uncertain	0.0030	D;D;.
Sift4G	Uncertain	0.0030	D;D;.
Polyphen		1.0	D;D;D
Vest4		0.97
MutPred		0.96		Gain of methylation at T86 (P = 0.0362);Gain of methylation at T86 (P = 0.0362);Gain of methylation at T86 (P = 0.0362);
MVP		0.99
MPC		0.30
ClinPred		1.0	D
GERP RS		5.3
Varity_R		0.97
gMVP		0.99

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: rs1291519904; hg19: chr13-20763464;