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NM_206933.4(USH2A):c.11954G>A (p.Trp3985Ter) AND Usher syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 17, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003226175.1

Allele description [Variation Report for NM_206933.4(USH2A):c.11954G>A (p.Trp3985Ter)]

NM_206933.4(USH2A):c.11954G>A (p.Trp3985Ter)

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.11954G>A (p.Trp3985Ter)
HGVS:
  • NC_000001.11:g.215728142C>T
  • NG_009497.2:g.700307G>A
  • NM_206933.4:c.11954G>AMANE SELECT
  • NP_996816.3:p.Trp3985Ter
  • NC_000001.10:g.215901484C>T
  • NG_009497.1:g.700255G>A
  • NM_206933.2:c.11954G>A
  • c.11954G>A
  • p.Trp3985X
Protein change:
W3985*
Links:
dbSNP: rs397517976
NCBI 1000 Genomes Browser:
rs397517976
Molecular consequence:
  • NM_206933.4:c.11954G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003922467Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Mar 17, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922467.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: USH2A c.11954G>A (p.Trp3985X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251330 control chromosomes (gnomAD). To our knowledge, no occurrence of c.11954G>A in individuals affected with Usher Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Apr 7, 2025