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_206933.4(USH2A):c.3407G>A (p.Ser1136Asn)

CA269917

133312 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 20e08ce1-8604-4189-b5ef-0d710ecff19c
Approved on: 2023-09-26
Published on: 2023-10-05

HGVS expressions

NM_206933.4:c.3407G>A
NM_206933.4(USH2A):c.3407G>A (p.Ser1136Asn)
NC_000001.11:g.216200031C>T
CM000663.2:g.216200031C>T
NC_000001.10:g.216373373C>T
CM000663.1:g.216373373C>T
NC_000001.9:g.214439996C>T
NG_009497.1:g.228366G>A
NG_009497.2:g.228418G>A
ENST00000307340.8:c.3407G>A
ENST00000674083.1:c.3407G>A
ENST00000307340.7:c.3407G>A
ENST00000366942.3:c.3407G>A
NM_007123.5:c.3407G>A
NM_206933.2:c.3407G>A
NM_206933.3:c.3407G>A
NM_007123.6:c.3407G>A
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Pathogenic

Met criteria codes 3
PM3_Very Strong PP4 PM2_Supporting
Not Met criteria codes 2
BP4 PP3

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.3407G>A variant in USH2A is a missense variant predicted to cause substitution of serine to asparagine at amino acid 1136. This variant is absent from large population studies (PM2_Supporting, gnomAD v2.1.1). The computational predictor REVEL gives a score of 0.466 which is neither above nor below the thresholds predicting a damaging or benign impact on USH2A function. This variant has been reported in at least 6 probands with USH2A-related disorders, including four individuals with autosomal recessive Usher syndrome and two individuals with isolated retinopathy. Of these individuals, the variant was confirmed in trans with a pathogenic variant in two individuals, but phase with a second pathogenic variant was unclear in the remaining 4 individuals (PM3_VeryStrong; PMID: 22135276, 25991456, 27957503, 36011334). Of note, the two individuals with isolated retinopathy harbored the pathogenic p.Cys759Phe variant, which is commonly found in individuals with an isolated retinopathy phenotype (SCV001334331.1). At least one patient with this variant was diagnosed with Usher syndrome (PP4). In summary, this variant meets the criteria to be classified as pathogenic for autosomal recessive USH2A-related disorders including Usher syndrome and isolated retinopathy based on ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP; PM2_Supporting, PM3_VeryStrong, PP4. (The ClinGen Hearing Loss VCEP Specifications Version 2; 09/26/2022)
Met criteria codes
PM3_Very Strong
TOTAL 4 POINTS, VERY STRONG FROM THE FOLLOWING 6 PROBANDS: Le Quesne Stabej 2012 (PMID 22135276) - Phenotype is Usher, 2nd variant p.Glu767SerfsX21 (Pathogenic), confirmed in trans, 1 point. Tang 2015 (PMID: 25991456) - Phenotype is Usher, 2nd variant p.Glu767SerfsX21 (Pathogenic), confirmed in trans, 1 point. Dad 2016 PMID: 27957503 (NEW) -- Phenotype is Usher, 2nd variant p.Glu767SerfsX21 (Pathogenic), unclear if confirmed in trans, 0.5 point. Feenstra 2022 PMID: 36011334 (NEW)- Phenotype is Usher, 2nd variant 14343+1G>C (abs gAD, in frame exon, 2 star pathogenic missense in ClinVar, LP), phase unclear, 0.5point Feenstra 2022 PMID: 36011334 (NEW) - Phenotype is RP, c.2276G>T p.(Cys759Phe) Known Path RP variant, phase unclear, 0.5point Feenstra 2022 PMID: 36011334 (NEW) - Phenotype is RP, c.2276G>T p.(Cys759Phe) Known Path RP variant, phase unclear, 0.5point
PP4
This variant has been identified in multiple patients with Usher syndrome type 2
PM2_Supporting
The variant is absent from gnomAD with adequate coverage.
Not Met criteria codes
BP4
The REVEL score is 0.466, which does not meet the cutoff for damaging or benign for hearing loss. Splicing predictors predict no effect.
PP3
The REVEL score is 0.466, which does not meet the cutoff for damaging or benign for hearing loss. Splicing predictors predict no effect.
Curation History
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