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

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Variant: NM_206933.3(USH2A):c.11713C>T (p.Arg3905Cys)

CA1393629

236537 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 1358e892-e818-4d36-8c8f-962217401ae3
Approved on: 2020-06-24
Published on: 2020-06-26

HGVS expressions

NM_206933.3:c.11713C>T
NM_206933.3(USH2A):c.11713C>T (p.Arg3905Cys)
NC_000001.11:g.215728383G>A
CM000663.2:g.215728383G>A
NC_000001.10:g.215901725G>A
CM000663.1:g.215901725G>A
NC_000001.9:g.213968348G>A
NG_009497.1:g.700014C>T
NG_009497.2:g.700066C>T
NM_206933.2:c.11713C>T
NM_206933.4:c.11713C>T
ENST00000307340.7:c.11713C>T
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Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP3 PP4 PM3_Strong
Not Met criteria codes 1
PM5

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.11713C>T (p.Arg3905Cys) variant in USH2A was present in 0.03281% (1/3048) of South Asian chromosomes in gnomAD v3, which is a low enough frequency to apply PM2_Supporting based on the thresholds defined for autosomal recessive hearing loss by the ClinGen Hearing Loss Expert Panel (PM2_Supporting; gnomad.broadinstitute.org). This variant has been reported in 3 individuals with Usher syndrome and a second pathogenic or likely pathogenic variant identified in USH2A, one of which was confirmed to be in trans with the p.Arg3905Cys variant (PM3_Strong; PMID: 28559085, 27208204, 31877679). At least one of these probands was confirmed to have both hearing loss and retinitis pigmentosa, features highly specific for Usher syndrome (PP4). The REVEL computational prediction tool produced a score of 0.8, which is above the threshold necessary to apply PP3. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel: PM3_Strong, PM2_Supporting, PP3, PP4.
Met criteria codes
PM2_Supporting
Present in 0.005026% (1/19896) of East Asian chromosomes in gnomAD v2. In v3, present in 0.03281% (1/3048) of South Asian chromosomes.
PP3
REVEL score 0.8. Not predicted to impact splicing. Cys is present in 1 other mammal in UCSC database (golden hamster).
PP4
1 proband with Usher syndrome had audio-vestibular testing and opthalmological examination.

PM3_Strong
Observed in 4 probands with Usher syndrome with second pathogenic/likely pathogenic variants identified, one of which was confirmed to be in trans (PMID: 28559085, 27208204, 31877679, 24944099).

Not Met criteria codes
PM5
One other variant in this codon, c.11714G>A (p.Arg3905His), is classified as VUS by 1 submitter only.
Curation History
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