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NM_206933.4(USH2A):c.3395G>A (p.Gly1132Asp)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Sep 30, 2021)
Last evaluated:
Apr 21, 2021
Accession:
VCV000166511.10
Variation ID:
166511
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.3395G>A (p.Gly1132Asp)

Allele ID
172913
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216200043 (GRCh38) GRCh38 UCSC
1: 216373385 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.216373385C>T
NC_000001.11:g.216200043C>T
NG_009497.1:g.228354G>A
... more HGVS
Protein change
G1132D
Other names
-
Canonical SPDI
NC_000001.11:216200042:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00260 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00049
The Genome Aggregation Database (gnomAD) 0.00216
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00238
The Genome Aggregation Database (gnomAD) 0.00246
Trans-Omics for Precision Medicine (TOPMed) 0.00199
Exome Aggregation Consortium (ExAC) 0.00064
Trans-Omics for Precision Medicine (TOPMed) 0.00220
1000 Genomes Project 0.00260
Links
ClinGen: CA179576
dbSNP: rs34596189
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 2 criteria provided, multiple submitters, no conflicts Nov 7, 2017 RCV000152625.1
Likely benign 4 criteria provided, multiple submitters, no conflicts Apr 21, 2021 RCV000894588.6
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001100644.1
Likely benign 2 criteria provided, single submitter Apr 27, 2017 RCV001100645.2
Uncertain significance 1 no assertion criteria provided Jan 1, 2015 RCV000504687.2
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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
USH2A-AS1 - - - GRCh38 - 337

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 07, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000854892.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(May 07, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000201938.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Gly1132Asp in Exon 17 of USH2A: This variant is not expected to have clinical si gnificance because it has been identified in 0.7% (27/3738) of … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001257173.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001257174.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Nov 16, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001038583.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 21, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001898957.1
Submitted: (Sep 19, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28704108, 30245029, 28041643, 26969326, 21738395, 25097241, 25262649)
Uncertain significance
(Jan 01, 2015)
no assertion criteria provided
Method: research
Usher syndrome, type 2D
Allele origin: unknown
NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV000598806.2
Submitted: (Apr 26, 2018)
Evidence details
Publications
PubMed (2)
Likely benign
(May 03, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001459760.1
Submitted: (Dec 28, 2020)
Evidence details
Uncertain significance
(-)
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: SCV001952477.1
Submitted: (Sep 30, 2021)
Evidence details
Uncertain significance
(-)
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: SCV001972161.1
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
Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. Carss KJ American journal of human genetics 2017 PMID: 28041643
Molecular epidemiology of Usher syndrome in Italy. Vozzi D Molecular vision 2011 PMID: 21738395
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=USH2A - - - -

Text-mined citations for rs34596189...

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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