The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_004004.6(GJB2):c.563A>G (p.Lys188Arg)

CA387460893

429984 (ClinVar)

Gene: GJB2
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 4695ee4b-08a2-4fd3-8d4a-f5d1dad3695c
Approved on: 2019-10-31
Published on: 2019-10-31

HGVS expressions

NM_004004.6:c.563A>G
NM_004004.6(GJB2):c.563A>G (p.Lys188Arg)
NC_000013.11:g.20189019T>C
CM000675.2:g.20189019T>C
NC_000013.10:g.20763158T>C
CM000675.1:g.20763158T>C
NC_000013.9:g.19661158T>C
NG_008358.1:g.8957A>G
ENST00000382844.2:c.563A>G
ENST00000382848.5:c.563A>G
ENST00000382844.1:c.563A>G
ENST00000382848.4:c.563A>G
NM_004004.5:c.563A>G
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Likely Pathogenic

Met criteria codes 3
PM3_Strong PP3 PM2
Not Met criteria codes 1
PS3

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The allele frequency of the c.563A>G (p.Lys188Arg) variant in GJB2 is 0.006% (1/15428) of European chromosomes by gnomAD, which is a low enough frequency to apply PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss (PM2). This variant has been detected in four probands patients with hearing loss (PMID 17666888, University of Minnesota internal data, GeneDx internal data). For two of those probands, a pathogenic was observed in trans, and in one individual a second pathogenic variant was observed but phase was not determined (PM3_Strong; PMID 17666888, University of Minnesota internal data, GeneDx internal data). The REVEL computational prediction analysis tool produced a score of 0.9, which is above the threshold necessary to apply PP3; however, this information is not predictive of pathogenicity on its own. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel (PM2, PM3_Strong, PP3).
Met criteria codes
PM3_Strong
2.5 points from 3 probands 1 proband reported in PMID 17666888 1 proband internal data from University of Minnesota internal data, p.Lys188Arg / p.Leu90Pro, trans phasing inferred from NGS data 1 proband internal data from GeneDx, p.Lys188Arg / c.35delG confirmed in trans

PP3
Revel score 0.969
PM2
0.006% (1/15428) of European alleles in gnomAD
Not Met criteria codes
PS3
HeLa cells transfected with Cx26 mutant vectors Fluorescence microscopy indicated that cells expressing Lys188Arg showed intracellular fluorescence (similar to S199F, path variant) Patterns indicate ER retention or cytoplasmic aggregation Indicative of mis-trafficking *Not one of our specified functional assays

Curation History
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