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NM_206933.4(USH2A):c.10712C>T (p.Thr3571Met) AND Usher syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 28, 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:
RCV003323372.2

Allele description [Variation Report for NM_206933.4(USH2A):c.10712C>T (p.Thr3571Met)]

NM_206933.4(USH2A):c.10712C>T (p.Thr3571Met)

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.10712C>T (p.Thr3571Met)
Other names:
NM_206933.2:c.10712C>T(p.Thr3571Met); NP_996816.3:p.(Thr3571Met)
HGVS:
  • NC_000001.11:g.215782070G>A
  • NG_009497.2:g.646379C>T
  • NM_206933.4:c.10712C>TMANE SELECT
  • NP_996816.3:p.Thr3571Met
  • NC_000001.10:g.215955412G>A
  • NG_009497.1:g.646327C>T
  • NM_206933.2:c.10712C>T
  • NM_206933.3:c.10712C>T
  • O75445:p.Thr3571Met
  • c.10712C>T
Protein change:
T3571M
Links:
UniProtKB: O75445#VAR_054604; dbSNP: rs202175091
NCBI 1000 Genomes Browser:
rs202175091
Molecular consequence:
  • NM_206933.4:c.10712C>T - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004029982Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Jul 28, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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Summary from all submissions

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

Citations

PubMed

Microarray-based mutation analysis of 183 Spanish families with Usher syndrome.

Jaijo T, Aller E, García-García G, Aparisi MJ, Bernal S, Avila-Fernández A, Barragán I, Baiget M, Ayuso C, Antiñolo G, Díaz-Llopis M, Külm M, Beneyto M, Nájera C, Millán JM.

Invest Ophthalmol Vis Sci. 2010 Mar;51(3):1311-7. doi: 10.1167/iovs.09-4085. Epub 2009 Aug 13.

PubMed [citation]
PMID:
19683999

An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients.

Bonnet C, Riahi Z, Chantot-Bastaraud S, Smagghe L, Letexier M, Marcaillou C, Lefèvre GM, Hardelin JP, El-Amraoui A, Singh-Estivalet A, Mohand-Saïd S, Kohl S, Kurtenbach A, Sliesoraityte I, Zobor D, Gherbi S, Testa F, Simonelli F, Banfi S, Fakin A, Glavač D, Jarc-Vidmar M, et al.

Eur J Hum Genet. 2016 Dec;24(12):1730-1738. doi: 10.1038/ejhg.2016.99. Epub 2016 Jul 27.

PubMed [citation]
PMID:
27460420
PMCID:
PMC5117943

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004029982.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: USH2A c.10712C>T (p.Thr3571Met) results in a non-conservative amino acid change located in the a fibronectin type III domain (IPR003961) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251304 control chromosomes (i.e., 3 heterozygotes; gnomAD v2.1 Exomes dataset). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.10712C>T has been reported in the literature in multiple compound heterozygous and homozygous individuals affected with Usher Syndrome (e.g., Jaijo_2010, Bonnet_2016). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 27460420, 19683999). Ten submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Dec 22, 2024