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


Variant: NM_004004.6(GJB2):c.339T>G (p.Ser113Arg)

CA342004

21385 (ClinVar)

Gene: GJB2
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 88473ffb-e617-4c19-af9c-0ca3bb39ff23

HGVS expressions

NM_004004.6:c.339T>G
NM_004004.6(GJB2):c.339T>G (p.Ser113Arg)
NC_000013.11:g.20189243A>C
CM000675.2:g.20189243A>C
NC_000013.10:g.20763382A>C
CM000675.1:g.20763382A>C
NC_000013.9:g.19661382A>C
NG_008358.1:g.8733T>G
ENST00000382844.2:c.339T>G
ENST00000382848.5:c.339T>G
ENST00000382844.1:c.339T>G
ENST00000382848.4:c.339T>G
NM_004004.5:c.339T>G

Uncertain Significance

Met criteria codes 2
PM3 PS3_Moderate
Not Met criteria codes 5
BP4 BA1 PP3 PM2 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.339T>G variant in GJB2 is a missense variant predicted to cause substitution of serine by arginine at amino acid 113. The highest population minor allele frequency in gnomAD v4.0.0 is 0.02% (7/26136 alleles) in the Ashkenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met). The computational predictor REVEL provides a score of 0.553 which is neither above nor below the thresholds predicting a damaging or benign impact on GJB2 function (PP3 and BP4 are not met). An in vitro functional study performed in Xenopus oocytes showed that variant junctional conductance for p.Ser113Arg was similar to water (negative control), indicating a loss of function impact on protein function (PS3_Moderate; PMID:12505163). The p.Ser113Arg variant has been reported in several probands with hearing loss, including 3 individuals with a second pathogenic variant without phase confirmation (1.5 points, PM3, PMID: 15365987, 11439000, 9529365, 16380907, 24078562). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for nonsyndromic genetic hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PS3_Moderate, PM3. (ClinGen Hearing Loss VCEP specifications version 2; 01/17/2024).
Met criteria codes
PM3
The p.Ser113Arg variant has been reported in several probands with hearing loss, and 3 individuals with a second pathogenic variant without phase confirmation (PM3, PMID: 15365987, 11439000, 9529365, 16380907, 24078562).
PS3_Moderate
An in vitro functional study performed in Xenopus oocytes showed that variant junctional conductance for p.Ser113Arg was similar to water (negative control), indicating a loss of function impact on protein function (PS3_Moderate; PMID:12505163).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002981 (3/10064 alleles) in the Ashkenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met).
PP3
REVEL: 0.553 (no criteria met)
PM2
The highest population minor allele frequency in gnomAD v4.0.0 is 0.0002678 (7/26136 alleles) in the Ashkenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met).
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002981 (3/10064 alleles) in the Ashkenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met).
Approved on: 2024-01-17
Published on: 2024-04-01
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