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NM_206933.4(USH2A):c.2792G>A (p.Cys931Tyr) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Oct 4, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001786059.4

Allele description [Variation Report for NM_206933.4(USH2A):c.2792G>A (p.Cys931Tyr)]

NM_206933.4(USH2A):c.2792G>A (p.Cys931Tyr)

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.2792G>A (p.Cys931Tyr)
HGVS:
  • NC_000001.11:g.216246602C>T
  • NG_009497.2:g.181847G>A
  • NM_007123.6:c.2792G>A
  • NM_206933.4:c.2792G>AMANE SELECT
  • NP_009054.6:p.Cys931Tyr
  • NP_996816.3:p.Cys931Tyr
  • NC_000001.10:g.216419944C>T
  • NG_009497.1:g.181795G>A
  • NM_206933.2:c.2792G>A
Protein change:
C931Y
Links:
dbSNP: rs145383772
NCBI 1000 Genomes Browser:
rs145383772
Molecular consequence:
  • NM_007123.6:c.2792G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_206933.4:c.2792G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002027831GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(May 18, 2021) 		germlineclinical testing

Citation Link,

SCV003513322Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 4, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

USH2A variants in Chinese patients with Usher syndrome type II and non-syndromic retinitis pigmentosa.

Zhu T, Chen DF, Wang L, Wu S, Wei X, Li H, Jin ZB, Sui R.

Br J Ophthalmol. 2021 May;105(5):694-703. doi: 10.1136/bjophthalmol-2019-315786. Epub 2020 Jul 16.

PubMed [citation]
PMID:
32675063

Multimodal imaging and genetic characteristics of Chinese patients with USH2A-associated nonsyndromic retinitis pigmentosa.

Chen C, Sun Q, Gu M, Qian T, Luo D, Liu K, Xu X, Yu S.

Mol Genet Genomic Med. 2020 Nov;8(11):e1479. doi: 10.1002/mgg3.1479. Epub 2020 Sep 6.

PubMed [citation]
PMID:
32893482
PMCID:
PMC7667352
See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV002027831.2

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

Description

Identified in a patient with retinitis pigmentosa in published literature (Xu et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In silico analysis suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 24938718, 32893482)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003513322.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 931 of the USH2A protein (p.Cys931Tyr). This variant is present in population databases (rs145383772, gnomAD 0.06%). This missense change has been observed in individual(s) with clinical features of inherited retinal dystrophy and/or retinitis pigmentosa (PMID: 32675063, 32893482). ClinVar contains an entry for this variant (Variation ID: 1325998). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt USH2A protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024