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NM_206933.4(USH2A):c.12093C>T (p.Tyr4031=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000048391.15
Variation ID:
48391
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.12093C>T (p.Tyr4031=)

Allele ID
57553
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 215680350 (GRCh38) GRCh38 UCSC
1: 215853692 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.215853692G>A
NC_000001.11:g.215680350G>A
NG_009497.1:g.748047C>T
... more HGVS
Protein change
-
Other names
p.Y4031Y:TAC>TAT
Canonical SPDI
NC_000001.11:215680349:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00215
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00292
The Genome Aggregation Database (gnomAD), exomes 0.00304
1000 Genomes Project 0.00080
Exome Aggregation Consortium (ExAC) 0.00295
The Genome Aggregation Database (gnomAD) 0.00295
Trans-Omics for Precision Medicine (TOPMed) 0.00315
Trans-Omics for Precision Medicine (TOPMed) 0.00307
Links
ClinGen: CA143281
dbSNP: rs55921307
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Feb 20, 2015 RCV000041713.6
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Dec 4, 2020 RCV000949878.6
Benign 1 no assertion criteria provided Sep 16, 2020 RCV001271127.1
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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
3406 4061

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 20, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000065409.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Tyr4031Tyr in exon 62 of USH2A: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, … (more)
Benign
(May 02, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169766.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Feb 20, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231882.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (4)
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001096150.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001147665.7
Submitted: (Jul 04, 2021)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001451978.1
Submitted: (Dec 28, 2020)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001925387.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959597.1
Submitted: (Sep 30, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001970048.1
Submitted: (Sep 21, 2021)
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
Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations. Garcia-Garcia G Orphanet journal of rare diseases 2011 PMID: 22004887
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
Mutation analysis in the long isoform of USH2A in American patients with Usher Syndrome type II. Yan D Journal of human genetics 2009 PMID: 19881469
Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II. Dreyer B Human mutation 2008 PMID: 18273898
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=USH2A - - - -

Text-mined citations for rs55921307...

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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 Nov 27, 2021