NM_206933.3(USH2A):c.11389+1del AND not provided

Clinical significance:Pathogenic (Last evaluated: Jul 15, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001208780.2

Allele description [Variation Report for NM_206933.3(USH2A):c.11389+1del]

NM_206933.3(USH2A):c.11389+1del

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.3(USH2A):c.11389+1del
HGVS:
  • NC_000001.11:g.215758595del
  • NG_009497.1:g.669803del
  • NM_206933.3:c.11389+1del
  • NC_000001.10:g.215931936delC
  • NC_000001.10:g.215931937del
  • NM_206933.2:c.11389+1delG
Links:
dbSNP: rs1414935620
NCBI 1000 Genomes Browser:
rs1414935620
Molecular consequence:
  • NM_206933.3:c.11389+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:
MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001380187Invitaecriteria provided, single submitter
Pathogenic
(Jul 15, 2019)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Genotype-phenotype correlation and mutation spectrum in a large cohort of patients with inherited retinal dystrophy revealed by next-generation sequencing.

Huang XF, Huang F, Wu KC, Wu J, Chen J, Pang CP, Lu F, Qu J, Jin ZB.

Genet Med. 2015 Apr;17(4):271-8. doi: 10.1038/gim.2014.138. Epub 2014 Nov 6.

PubMed [citation]
PMID:
25356976

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV001380187.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change affects a donor splice site in intron 58 of the USH2A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). Disruption of this splice site has been observed in individual(s) with inherited retinal dystrophy (PMID: 25356976). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 558520). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 8, 2021

Support Center