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NM_206933.4(USH2A):c.9570+1G>T AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 17, 2022
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:
RCV002857091.2

Allele description [Variation Report for NM_206933.4(USH2A):c.9570+1G>T]

NM_206933.4(USH2A):c.9570+1G>T

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.9570+1G>T
HGVS:
  • NC_000001.11:g.215816996C>A
  • NG_009497.2:g.611453G>T
  • NM_206933.4:c.9570+1G>TMANE SELECT
  • NC_000001.10:g.215990338C>A
Molecular consequence:
  • NM_206933.4:c.9570+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV003222030Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 17, 2022) 		germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.

Huang XF, Xiang P, Chen J, Xing DJ, Huang N, Min Q, Gu F, Tong Y, Pang CP, Qu J, Jin ZB.

PLoS One. 2013 May 30;8(5):e63832. doi: 10.1371/journal.pone.0063832. Print 2013.

PubMed [citation]
PMID:
23737954
PMCID:
PMC3667821

Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing.

Yang T, Wei X, Chai Y, Li L, Wu H.

Orphanet J Rare Dis. 2013 Jun 14;8:85. doi: 10.1186/1750-1172-8-85.

PubMed [citation]
PMID:
23767834
PMCID:
PMC3703291
See all PubMed Citations (8)

Details of each submission

From Invitae, SCV003222030.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individual(s) with USH2A-related conditions and/or Usher syndrome (PMID: 23737954, 23767834). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 48 of the USH2A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site 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).

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

Last Updated: Feb 20, 2024