rs200104362

chr13-20189079-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1 BP4_Strong

The NM_004004.6(GJB2):c.503A>G(p.Lys168Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,614,060 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. K168K) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00066 (1 hom., cov: 33)
  • Exomes 𝑓: 0.000052 (1 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7 B:1
• Conservation: PhyloP100: 7.97

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 Likely_benign. Variant got -2 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 6 uncertain in NM_004004.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.031392753).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.503A>G	p.Lys168Arg	missense_variant	2/2	ENST00000382848.5
GJB2	XM_011535049.3	c.503A>G	p.Lys168Arg	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.503A>G	p.Lys168Arg	missense_variant	2/2	1	NM_004004.6	P1
GJB2	ENST00000382844.2	c.503A>G	p.Lys168Arg	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.000664 AC: 101 AN: 152184 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00570

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00382

GnomAD3 exomes AF: 0.0000518 AC: 13 AN: 251060 Hom.: 0 AF XY: 0.0000589 AC XY: 8 AN XY: 135734

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000260

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000881

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.0000520 AC: 76 AN: 1461758 Hom.: 1 Cov.: 33 AF XY: 0.0000385 AC XY: 28 AN XY: 727162

Gnomad4 AFR exome AF: 0.0000896

Gnomad4 AMR exome AF: 0.000961

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.000464

GnomAD4 genome AF: 0.000663 AC: 101 AN: 152302 Hom.: 1 Cov.: 33 AF XY: 0.000685 AC XY: 51 AN XY: 74478

Gnomad4 AFR AF: 0.000144

Gnomad4 AMR AF: 0.00569

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00378

Alfa AF: 0.0000977 Hom.: 0

Bravo AF: 0.00128

ExAC AF: 0.0000741 AC: 9

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:7 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 12, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jul 16, 2022	This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 168 of the GJB2 protein (p.Lys168Arg). This variant is present in population databases (rs200104362, gnomAD 0.04%). This missense change has been observed in individual(s) with clinical features of GJB2-related conditions (PMID: 17357124, 21728791, 23684175). ClinVar contains an entry for this variant (Variation ID: 44756). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Sep 26, 2023	Observed in several unrelated patients with apparently non-syndromic hearing loss in published literature, often as a single heterozygous variant (Samanich et al., 2007; Batissoco et al., 2009; Tsukada et al., 2010; da Silva-Costa et al, 2011; Manzoli et al., 2013); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 19283857, 20022641, 30245029, 32387678, 19081147, 25262649, 17357124, 25388846, 17567889, 19125024, 20497192, 23684175, 21728791, 29773520, 33096615, 24158611, 24156272, 20381175, 19887791, 19230829, 17666888) -

not specified Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 11, 2018	The GJB2 c.503A>G; p.Lys168Arg variant (rs200104362) has been reported in multiple individuals in hearing loss cohorts; however, inheritance and specific clinical information were not provided for these individuals (Batissoco 2009, Manzoli 2013, Samanich 2007, Shearer 2014). The p.Lys168Arg variant is reported in ClinVar (Variant ID: 44756) and is found in the general population with an overall allele frequency of 0.005% (15/282,470 alleles) in the Genome Aggregation Database. The lysine at codon 168 is highly conserved, but computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. Given the lack of clinical and functional data, the significance of the p.Lys168Arg variant is uncertain at this time. References: Batissoco et al. Prevalence of GJB2 (connexin-26) and GJB6 (connexin-30) mutations in a cohort of 300 Brazilian hearing-impaired individuals: implications for diagnosis and genetic counseling. Ear Hear. 2009 Feb;30(1):1-7. doi: 10.1097/AUD.0b013e31819144ad. Manzoli et al. Non-syndromic hearing impairment in a multi-ethnic population of Northeastern Brazil. Int J Pediatr Otorhinolaryngol. 2013 Jul;77(7):1077-82. doi: 10.1016/j.ijporl.2013.04.001. Epub 2013 May 15. Samanich et al. Mutations in GJB2, GJB6, and mitochondrial DNA are rare in African American and Caribbean Hispanic individuals with hearing impairment. Am J Med Genet A. 2007 Apr 15;143A(8):830-8. Shearer et al. Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants. Am J Hum Genet. 2014 Oct 2;95(4):445-53. doi: 10.1016/j.ajhg.2014.09.001. Epub 2014 Sep 25. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 18, 2019	Variant classified as Uncertain Significance - Favor Benign. The p.Lys168Arg variant in GJB2 has been previously reported in >20 individuals with hearing loss, primarily of Brazilian or Latino ancestry (Batisscoco 2009, Christiani 2007, Dalamon 2013, Felix 2019, Fischer 2009, Gravina 2010, Manzoli 2013, Martins 2013, Putcha 2007, Samanich 2007, Shan 2010, Tsukada 2010). However, the variant has not been reported in the homozygous or compound heterozygous state. It has been identified in 0.03% (10/35418) of Latino chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, while the clinical significance of this variant is uncertain, the computational data and the fact that none of the probands had a second variant identified on the other copy of the gene suggests that the variant is more likely benign. ACMG/AMP criteria applied: PM2_Supporting, BP4. -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 29, 2022	Variant summary: GJB2 c.503A>G (p.Lys168Arg) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00067 in 152268 control chromosomes, predominantly at a frequency of 0.0057 within the Latino subpopulation in the gnomAD v3.1.1 database, including 1 homozygote. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 17-fold of the estimated maximal expected allele frequency for a pathogenic variant in GJB2 causing Non-Syndromic Hearing Loss phenotype (0.00034), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. c.503A>G has been reported in the literature in the heterozygous state without any other GJB2 pathogenic variants in individuals affected with Non-Syndromic Hearing Loss (e.g. Christiani_2007, Putcha_2007, Samanich_2007, Batissoco_2009, Tsukada_2010, da Silva-Costa_2011, Dalamon_2013, Felix_2019, Figueroa-Ildefonso_2019, Buonfiglio_2020) but it was also reported in unaffected/control individuals (e.g. Samanich_2007, da Silva-Costa_2011). These reports do not provide unequivocal conclusions about association of the variant with Non-Syndromic Hearing Loss. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. However, c.503A>G was expert-curated as Likely benign in the Deafness Variation Database (Azaiez_2018). Based on the evidence outlined above, the variant was classified as likely benign. -

Autosomal recessive nonsyndromic hearing loss 1A Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

May 09, 2017

- -

Nonsyndromic genetic hearing loss Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

INGEBI, INGEBI / CONICET

Aug 31, 2020

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of c.503A>G, p.(Lys168Arg) variant in GJB2 gene is 0,015% (10/35418 Latino alleles 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 criteria to apply to PM2_Supporting rule. Computational evidence predicted a pathogenic effect of the mutation to the protein (REVELscore: 0.720) applying to PP3 criteria. The p.(Lys168Arg) change has been identified only in heterozygous state in several patients (PMID: 17567889, 19125024, 20381175, 20497192, 21728791, 24156272, 19887791). Therefore, the clinical significance of this variant is currently uncertain (PM2_Supporting, PP3). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Benign	22
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.70	D;D;D
Eigen	Benign	0.12
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Pathogenic	0.97	D
MetaRNN	Benign	0.031	T;T;T
MetaSVM	Uncertain	0.44	D
MutationAssessor	Benign	2.0	M;M;M
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-1.8	N;N;.
REVEL	Pathogenic	0.72
Sift	Benign	0.24	T;T;.
Sift4G	Benign	0.31	T;T;.
Polyphen		0.074	B;B;B
Vest4		0.55
MVP		0.91
MPC		0.048
ClinPred		0.19	T
GERP RS		5.5
Varity_R		0.42
gMVP		0.84

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: rs200104362; hg19: chr13-20763218;