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

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Apr 27, 2017
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:
RCV000504801.14

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:
Retinitis pigmentosa (RP)
Synonyms:
Tapetoretinal degeneration
Identifiers:
MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001257283Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Apr 27, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
Europeanunknownyes1not providednot provided1not providedresearch

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

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.

Carss KJ, Arno G, Erwood M, Stephens J, Sanchis-Juan A, Hull S, Megy K, Grozeva D, Dewhurst E, Malka S, Plagnol V, Penkett C, Stirrups K, Rizzo R, Wright G, Josifova D, Bitner-Glindzicz M, Scott RH, Clement E, Allen L, Armstrong R, Brady AF, et al.

Am J Hum Genet. 2017 Jan 5;100(1):75-90. doi: 10.1016/j.ajhg.2016.12.003. Epub 2016 Dec 29.

PubMed [citation]
PMID:
28041643
PMCID:
PMC5223092
See all PubMed Citations (3)

Details of each submission

From NIHR Bioresource Rare Diseases, University of Cambridge, SCV000598801.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European1not providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001257283.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000598801NIHR Bioresource Rare Diseases, University of Cambridge
flagged submission
Reason: Conflicts with expert reviewed submission without evidence to support different classification
Notes: None
Likely pathogenic
(Jan 1, 2015) 		unknownresearch

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

Last Updated: Nov 10, 2024