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NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr) AND Usher syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Dec 24, 2020
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV001775076.10

Allele description [Variation Report for NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr)]

NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr)

Genes:
LOC122152296:Sharpr-MPRA regulatory region 8762 [Gene]
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.2522C>A (p.Ser841Tyr)
Other names:
NM_206933.2(USH2A):c.2522C>A
HGVS:
  • NC_000001.11:g.216246872G>T
  • NG_009497.2:g.181577C>A
  • NG_076570.1:g.246G>T
  • NM_007123.6:c.2522C>A
  • NM_206933.4:c.2522C>AMANE SELECT
  • NP_009054.5:p.Ser841Tyr
  • NP_009054.6:p.Ser841Tyr
  • NP_996816.2:p.Ser841Tyr
  • NP_996816.3:p.Ser841Tyr
  • NC_000001.10:g.216420214G>T
  • NG_009497.1:g.181525C>A
  • NM_007123.5:c.2522C>A
  • NM_206933.2:c.2522C>A
  • NM_206933.3:c.2522C>A
  • O75445:p.Ser841Tyr
  • c.2522C>A
Protein change:
S841Y
Links:
UniProtKB: O75445#VAR_025777; dbSNP: rs111033282
NCBI 1000 Genomes Browser:
rs111033282
Molecular consequence:
  • NM_007123.6:c.2522C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206933.4:c.2522C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Usher syndrome
Synonyms:
Usher Syndromes; Usher's syndrome
Identifiers:
MONDO: MONDO:0019501; MeSH: D052245; MedGen: C0271097; Orphanet: 886; OMIM: PS276900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000927009ClinGen Hearing Loss Variant Curation Expert Panel
reviewed by expert panel

(ClinGen HL ACMG Specifications v1)		Benign
(Dec 24, 2020) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Hearing Loss Variant Curation Expert Panel, SCV000927009.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The p.Ser841Tyr variant in the USH2A gene has been identified in three individuals with Usher syndrome (PMIDs 19683999, 28944237, 28653555); however, in two of those individuals a variant on the second allele was not identified (PMIDs 19683999, 28944237) and in one (PMID 28653555), the variant found on the other alleles (p.Tyr1992Cys) did not have evidence to support pathogenicity and has a high allele frequency in gnomAD (of European (Finnish) chromosomes). The filtering allele frequency of the p.Ser841Tyr variant in the USH2A gene is 1.4% for European (Finnish) chromosomes by gnomAD (1144/128242 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1).

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

Last Updated: Nov 3, 2024