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NM_206933.3(USH2A):c.9921T>G (p.Cys3307Trp)

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
7 (Most recent: Sep 29, 2021)
Last evaluated:
Oct 23, 2019
Accession:
VCV000226441.12
Variation ID:
226441
Description:
single nucleotide variant
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NM_206933.3(USH2A):c.9921T>G (p.Cys3307Trp)

Allele ID
228240
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 215798944 (GRCh38) GRCh38 UCSC
1: 215972286 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_206933.3(USH2A):c.9921T>G
NC_000001.10:g.215972286A>C
NC_000001.11:g.215798944A>C
... more HGVS
Protein change
C3307W
Other names
-
Canonical SPDI
NC_000001.11:215798943:A:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA16044155
dbSNP: rs1057519382
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 reviewed by expert panel Oct 23, 2019 RCV001004786.1
Uncertain significance 1 criteria provided, single submitter Dec 12, 2017 RCV000675100.1
Uncertain significance 1 criteria provided, single submitter Apr 8, 2021 RCV001376499.1
Uncertain significance 1 criteria provided, single submitter Apr 1, 2021 RCV001723791.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 20, 2020 RCV001056911.4
Likely pathogenic 1 no assertion criteria provided May 19, 2016 RCV000216234.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
USH2A - - GRCh38
GRCh37
3426 4025

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 23, 2019)
reviewed by expert panel
Method: curation
Usher syndrome
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen Hearing Loss Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV001164271.1
Submitted: (Nov 01, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.9921T>G (p.Cys3307Trp) variant in USH2A is absent from gnomAD (PM2). This variant was observed in 1 patient with Usher Syndrome, without a second variant … (more)
Uncertain significance
(Dec 12, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Retinitis pigmentosa 39
Allele origin: unknown
Counsyl
Accession: SCV000800635.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Uncertain significance
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001221376.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces cysteine with tryptophan at codon 3307 of the USH2A protein (p.Cys3307Trp). The cysteine residue is highly conserved and there is a … (more)
Uncertain significance
(Apr 08, 2021)
criteria provided, single submitter
Method: research
Retinitis pigmentosa 39
Allele origin: germline
Ocular Genomics Institute, Massachusetts Eye and Ear
Accession: SCV001573670.1
Submitted: (Apr 26, 2021)
Evidence details
Publications
PubMed (2)
Comment:
The USH2A c.9921T>G variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we … (more)
Uncertain significance
(Apr 01, 2021)
criteria provided, single submitter
Method: curation
Retinitis pigmentosa
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001950418.1
Submitted: (Sep 29, 2021)
Evidence details
Publications
PubMed (2)
Comment:
The p.Cys3307Trp variant in USH2A was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics … (more)
Pathogenic
(Apr 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001246989.6
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(May 19, 2016)
no assertion criteria provided
Method: literature only
Usher syndrome type 1
Allele origin: germline
GeneReviews
Accession: SCV000268766.1
Submitted: (May 19, 2016)
Evidence details
Publications
PubMed (1)
Other databases
http://www.ncbi.nlm.nih.gov/book…

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Usher Syndrome Type I Koenekoop RK - 2020 PMID: 20301442
Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Stone EM Ophthalmology 2017 PMID: 28559085
NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa. Ge Z Scientific reports 2015 PMID: 26667666
Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis. Bonnet C Orphanet journal of rare diseases 2011 PMID: 21569298
http://www.ncbi.nlm.nih.gov/books/NBK1265/ - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/f41fc1cd-9f60-4c2d-ae7d-a2b577765994 - - - -

Text-mined citations for rs1057519382...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021