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NM_206933.4(USH2A):c.11241C>A (p.Tyr3747Ter)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
5 (Most recent: Aug 20, 2021)
Last evaluated:
Sep 17, 2018
Accession:
VCV000506273.8
Variation ID:
506273
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.11241C>A (p.Tyr3747Ter)

Allele ID
496182
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 215758743 (GRCh38) GRCh38 UCSC
1: 215932085 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NG_009497.1:g.669654C>A
NG_009497.2:g.669706C>A
NM_206933.4:c.11241C>A MANE Select NP_996816.3:p.Tyr3747Ter nonsense
... more HGVS
Protein change
Y3747*
Other names
NM_206933.2(USH2A):c.11241C>A(p.Tyr3747Ter)
NM_206933.2(USH2A):c.11241C>A
Canonical SPDI
NC_000001.11:215758742:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA1393780
dbSNP: rs777465132
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 reviewed by expert panel Sep 17, 2018 RCV000710334.1
Pathogenic 2 criteria provided, multiple submitters, no conflicts Dec 14, 2019 RCV001057761.5
Pathogenic 1 criteria provided, single submitter Jan 30, 2018 RCV000605356.1
Pathogenic 1 no assertion criteria provided Sep 16, 2020 RCV001271137.1
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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
3452 4058

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 17, 2018)
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: SCV000840528.3
Submitted: (Feb 27, 2019)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
The p.Tyr3747X variant in USH2A is predicted to cause a premature stop codon in biologically-relevant-exon 58/72 that leads to a truncated or absent protein in … (more)
Pathogenic
(Jan 30, 2018)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000713838.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
The p.Tyr3747X variant in USH2A has not been previously reported in individuals with hearing loss or Usher syndrome, but has been identified in 0.02% (4/24020) … (more)
Pathogenic
(Dec 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001222271.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Tyr3747*) in the USH2A gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Aug 27, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001803549.1
Submitted: (Aug 20, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001451990.1
Submitted: (Dec 28, 2020)
Evidence details

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
A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies. Ezquerra-Inchausti M Scientific reports 2018 PMID: 30337596
A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants. Lenassi E European journal of human genetics : EJHG 2015 PMID: 25649381
Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa. McGee TL Journal of medical genetics 2010 PMID: 20507924
Identification of novel USH2A mutations: implications for the structure of USH2A protein. Dreyer B European journal of human genetics : EJHG 2000 PMID: 10909849
Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. Weston MD American journal of human genetics 2000 PMID: 10729113
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/b7a55bd1-1f82-499f-acdf-a7a6884c636c - - - -

Text-mined citations for rs777465132...

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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 30, 2021