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NM_206933.4(USH2A):c.2809+2T>A AND Rare genetic deafness

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 20, 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:
RCV000605844.4

Allele description [Variation Report for NM_206933.4(USH2A):c.2809+2T>A]

NM_206933.4(USH2A):c.2809+2T>A

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.2809+2T>A
HGVS:
  • NC_000001.11:g.216246583A>T
  • NG_009497.2:g.181866T>A
  • NG_076570.2:g.201A>T
  • NM_007123.6:c.2809+2T>A
  • NM_206933.4:c.2809+2T>AMANE SELECT
  • NC_000001.10:g.216419925A>T
  • NM_206933.2:c.2809+2T>A
Links:
dbSNP: rs1553320397
NCBI 1000 Genomes Browser:
rs1553320397
Molecular consequence:
  • NM_007123.6:c.2809+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_206933.4:c.2809+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Name:
Rare genetic deafness
Identifiers:
MedGen: C5680250; Orphanet: 96210

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000731690Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Pathogenic
(Jun 20, 2017) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000731690.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.2809+2T>A variant in USH2A has not been previously reported in individuals with hearing loss or Usher syndrome and is absent from large population databas es. This variant occurs in the invariant region (+/- 1,2) of the splice consensu s sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Loss of function is an established disease mechanism for autosom al recessive Usher syndrome. In summary, the c.2809+2T>A variant meets criteria to be classified as pathogenic for autosomal recessive Usher syndrome based on the predicted impact to splicing.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Sep 29, 2024