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NM_004004.6(GJB2):c.385G>A (p.Glu129Lys) AND Autosomal recessive nonsyndromic hearing loss 1A

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Sep 12, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001089545.4

Allele description [Variation Report for NM_004004.6(GJB2):c.385G>A (p.Glu129Lys)]

NM_004004.6(GJB2):c.385G>A (p.Glu129Lys)

Gene:
GJB2:gap junction protein beta 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q12.11
Genomic location:
Preferred name:
NM_004004.6(GJB2):c.385G>A (p.Glu129Lys)
HGVS:
  • NC_000013.11:g.20189197C>T
  • NG_008358.1:g.8779G>A
  • NM_004004.6:c.385G>AMANE SELECT
  • NP_003995.2:p.Glu129Lys
  • LRG_1350t1:c.385G>A
  • LRG_1350:g.8779G>A
  • LRG_1350p1:p.Glu129Lys
  • NC_000013.10:g.20763336C>T
  • NM_004004.5:c.385G>A
  • P29033:p.Glu129Lys
  • c.385G>A
Protein change:
E129K
Links:
UniProtKB: P29033#VAR_023611; dbSNP: rs397516875
NCBI 1000 Genomes Browser:
rs397516875
Molecular consequence:
  • NM_004004.6:c.385G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 1A (DFNB1A)
Synonyms:
Deafness nonsyndromic, Connexin 26 linked; Deafness, autosomal recessive 1A; DFNB 1 Nonsyndromic Hearing Loss and Deafness; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009076; MedGen: C2673759; Orphanet: 90636; OMIM: 220290

Recent activity

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001244784Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 12, 2017) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001463370Natera, Inc.
no assertion criteria provided
Uncertain significance
(Sep 16, 2020) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001244784.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A heterozygous missense variant was identified, NM_004004.5(GJB2):c.385G>A in exon 2 of the GJB2 gene. This substitution creates a minor amino acid change from an glutamic acid to a lysine at position 129, NP_003995.2(GJB2):p.(Glu129Lys). The glutamic acid at this position has low conservation (100 vertebrates, UCSC). In silico predictions of the pathogenicity of this variant are conflicting (Polyphen, SIFT, CADD, Mutation Taster). This variant has been previously observed in other deafness cases (Kenna, MA. et al. (2001), Dalamon, V. et al. (2005), Wu, B-L. et al. (2002) and Toth, T. et al. (2007)) and reported as PATHOGENIC in the Deafness Variation Database but evidence for its pathogenicity is conflicting and it is designated as a variant of uncertain significance in ClinVar. This variant is present in the gnomAD population database at a frequency of 0.0057% (14/245256, 0 hom). It is not situated in a known functional domain. The homozygous presence of the NM_004004.5(GJB2):c.101T>C variant in the same patient suggests that this variant (NM_004004.5(GJB2):c.385G>A) is in cis with one of the alleles. Based on current information, this variant has been classified as a VARIANT of UNKNOWN SIGNIFICANCE (VUS).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001463370.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024