NM_206933.3(USH2A):c.6446C>A (p.Pro2149Gln) AND Usher syndrome

Clinical significance:Likely pathogenic (Last evaluated: May 26, 2020)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001171538.1

Allele description [Variation Report for NM_206933.3(USH2A):c.6446C>A (p.Pro2149Gln)]

NM_206933.3(USH2A):c.6446C>A (p.Pro2149Gln)

Gene:
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.3(USH2A):c.6446C>A (p.Pro2149Gln)
HGVS:
  • NC_000001.11:g.216000442G>T
  • NG_009497.1:g.427955C>A
  • NM_206933.3:c.6446C>A
  • NP_996816.2:p.Pro2149Gln
  • NC_000001.10:g.216173784G>T
  • NM_206933.2:c.6446C>A
  • NM_206933.3(USH2A):c.6446C>A
  • p.Pro2149Gln
Protein change:
P2149Q
Links:
dbSNP: rs869312182
NCBI 1000 Genomes Browser:
rs869312182
Molecular consequence:
  • NM_206933.3:c.6446C>A - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001334323ClinGen Hearing Loss Variant Curation Expert Panelreviewed by expert panel
Likely pathogenic
(May 26, 2020)
germlinecuration

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.

Ellingford JM, Horn B, Campbell C, Arno G, Barton S, Tate C, Bhaskar S, Sergouniotis PI, Taylor RL, Carss KJ, Raymond LFL, Michaelides M, Ramsden SC, Webster AR, Black GCM.

J Med Genet. 2018 Feb;55(2):114-121. doi: 10.1136/jmedgenet-2017-104791. Epub 2017 Oct 26.

PubMed [citation]
PMID:
29074561
PMCID:
PMC5800348

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 ClinGen Hearing Loss Variant Curation Expert Panel, SCV001334323.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (3)

Description

The c.6446C>A (p.Pro2149Gln) variant in USH2A was absent from gnomAD (PM2). It has been detected in one patient with Usher syndrome and one patient with isolated Retinitis pigmentosa, both of whom carried another suspected pathogenic variant in trans (PM3_Strong; PP4; PMIDs: 26872967, 29074561, 28041643; ClinVar ID: 2356). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel: PM2, PM3_Strong, PP4.

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

Last Updated: Oct 7, 2021

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