rs111033194

chr13-20188912-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1 BP4_Moderate

The NM_004004.6(GJB2):c.670A>C(p.Lys224Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,613,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. K224K) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00017 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:9
• Conservation: PhyloP100: 3.53

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 Uncertain_significance. Variant got 0 ACMG points.

• PM1: In a chain Gap junction beta-2 protein (size 225) in uniprot entity CXB2_HUMAN there are 218 pathogenic changes around while only 32 benign (87%) in NM_004004.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.16398773).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.670A>C	p.Lys224Gln	missense_variant	2/2	ENST00000382848.5
GJB2	XM_011535049.3	c.670A>C	p.Lys224Gln	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.670A>C	p.Lys224Gln	missense_variant	2/2	1	NM_004004.6	P1
GJB2	ENST00000382844.2	c.670A>C	p.Lys224Gln	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.000171 AC: 26 AN: 152216 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000133 AC: 33 AN: 247742 Hom.: 0 AF XY: 0.000126 AC XY: 17 AN XY: 134628

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000174

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: 0.000225

Gnomad OTH exome AF: 0.000329

GnomAD4 exome AF: 0.000146 AC: 213 AN: 1460800 Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 98 AN XY: 726704

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.000268

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: 0.000155

Gnomad4 OTH exome AF: 0.000397

GnomAD4 genome AF: 0.000171 AC: 26 AN: 152334 Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5 AN XY: 74498

Gnomad4 AFR AF: 0.0000962

Gnomad4 AMR AF: 0.000392

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000191

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000199 Hom.: 0

Bravo AF: 0.000234

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000117 AC: 1

ExAC AF: 0.0000907 AC: 11

EpiCase AF: 0.000218

EpiControl AF: 0.000415

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 24, 2023	Variant summary: GJB2 c.670A>C (p.Lys224Gln) 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 0.00014 in 250298 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in GJB2 causing Autosomal Recessive Non-Syndromic Hearing Loss (0.00014 vs 0.025), allowing no conclusion about variant significance. c.670A>C has been reported in the literature in multiple individuals affected with non-syndromic hearing loss, including both heterozygous individuals without a second variant identified and homozygous individuals (Tekin_2007, Ozylmaz_2019) without evidence of cosegregation with disease provided. These reports do not provide unequivocal conclusions about association of the variant with Autosomal Recessive Non-Syndromic Hearing Loss. One publication reports experimental evidence evaluating an impact on protein function (Spagnol_2016), however it does not allow convincing conclusions about the variant effect. The following publications have been ascertained in the context of this evaluation (PMID: 17366579, 22567369, 12865758, 17666888, 19230829, 20381175, 23695287, 19081147, 17357124, 22016077, 10874298, 26542351, 31620696, 30245029). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Additionally, a published expert curation also classified the variant as uncertain significance (Deafness Variation Database, Azaiez_2018). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 04, 2018	The p.Lys224Gln variant in GJB2 has been previously reported in 8 individuals wi th hearing loss (Antoniadi 2000, Pandya 2003, Samanich 2007, Kokotas 2010, Shan 2010, LMM data); however a variant affecting the remaining DFNB1 allele (GJB2 a nd GJB6 genes) was not identified in any of the individuals. This variant has be en identified in 27/124038 European chromosomes and in 5/34358 Latino chromosome s by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs111033194), though, this frequency is not high enough to rule out a path ogenic role. Computational prediction tools and conservation analyses do not pro vide strong support for or against an impact to the protein. In summary, the cli nical significance of the p.Lys224Gln variant is uncertain. ACMG/AMP Criteria ap plied: None. -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Dec 24, 2018	The GJB2 c.670A>C; p.Lys224Gln variant (rs111033194) is reported in the literature in individuals with hearing loss and in several normal-hearing controls (Antoniadi 2000, Matos 2011, Pandya 2003, Putcha 2007, Samanich 2007). This variant does not exhibit dominant inheritance (Antoniadi 2000), and, to our knowledge, it has not been reported in trans to another pathogenic variant in affected individuals (Antoniadi 2000, Pandya 2003, Putcha 2007, Samanich 2007). This variant is reported in ClinVar (Variation ID: 44765), and it is found in the general population with an overall allele frequency of 0.01% (36/279154 alleles) in the Genome Aggregation Database. The lysine at codon 224 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.Lys224Gln variant is uncertain at this time. References: Antoniadi T et al. Mutation analysis of the GJB2 (connexin 26) gene by DGGE in Greek patients with sensorineural deafness. Hum Mutat. 2000;16(1):7-12. Matos TD et al. Assessing Noncoding Sequence Variants of GJB2 for Hearing Loss Association. Genet Res Int. 2011;2011:827469. Pandya A et al. Frequency and distribution of GJB2 (connexin 26) and GJB6 (connexin 30) mutations in a large North American repository of deaf probands. Genet Med. 2003 Jul-Aug;5(4):295-303. Putcha GV et al. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. Genet Med. 2007 Jul;9(7):413-26. Samanich J 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. -

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 24, 2023	Observed in the heterozygous state without a second variant in multiple individuals with hearing loss in the published literature (Antoniadi et al., 2000; Pandya et al., 2003; Samanich et al., 2007; Shan et al., 2010); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 19230829, 17357124, 12172392, 25262649, 25388846, 26990548, 30245029, 19081147, 26542351, 20059378, 17666888, 17366579, 16125251, 22567369, 21844220, 20381175, 12865758, 31620696, 33199029, 17444514, 10874298) -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Oct 12, 2022	This sequence change replaces lysine, which is basic and polar, with glutamine, which is neutral and polar, at codon 224 of the GJB2 protein (p.Lys224Gln). This variant is present in population databases (rs111033194, gnomAD 0.02%). This missense change has been observed in individual(s) with autosomal recessive deafness (PMID: 17444514). ClinVar contains an entry for this variant (Variation ID: 44765). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GJB2 protein function. 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	Athena Diagnostics	Mar 23, 2018	- -

Autosomal recessive nonsyndromic hearing loss 1A Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Mar 30, 2017	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1844678:X-linked mixed hearing loss with perilymphatic gusher;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Uncertain	0.099	D
BayesDel_noAF	Pathogenic	0.19
Cadd	Benign	21
Dann	Benign	0.95
DEOGEN2	Benign	0.20	T;T;T
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.11
FATHMM_MKL	Uncertain	0.86	D
M_CAP	Uncertain	0.090	D
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Uncertain	0.67	D
MutationAssessor	Benign	1.5	L;L;L
MutationTaster	Benign	0.95	D;D
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.67	N;N;.
REVEL	Uncertain	0.53
Sift	Benign	0.094	T;T;.
Sift4G	Benign	0.15	T;T;.
Polyphen		0.037	B;B;B
Vest4		0.25
MVP		0.94
MPC		0.041
ClinPred		0.049	T
GERP RS		5.7
Varity_R		0.16
gMVP		0.64

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: rs111033194; hg19: chr13-20763051;