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NM_206933.4(USH2A):c.1876C>T (p.Arg626Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Aug 30, 2021
Accession:
VCV000497414.21
Variation ID:
497414
Description:
single nucleotide variant
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NM_206933.4(USH2A):c.1876C>T (p.Arg626Ter)

Allele ID
488838
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216289375 (GRCh38) GRCh38 UCSC
1: 216462717 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.216462717G>A
NC_000001.11:g.216289375G>A
NG_009497.1:g.139022C>T
... more HGVS
Protein change
R626*
Other names
-
Canonical SPDI
NC_000001.11:216289374:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA1396371
dbSNP: rs534534437
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Aug 30, 2021 RCV000599059.6
Pathogenic 1 criteria provided, single submitter Mar 19, 2019 RCV000592080.4
Pathogenic 1 criteria provided, single submitter Jun 19, 2019 RCV001074303.1
Pathogenic 1 criteria provided, single submitter Apr 8, 2021 RCV001376324.1
Pathogenic 1 no assertion criteria provided Sep 16, 2020 RCV001271237.1
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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
(Oct 04, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000701902.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Mar 19, 2019)
criteria provided, single submitter
Method: clinical testing
Usher syndrome
(Autosomal recessive inheritance)
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000710847.3
Submitted: (Jun 03, 2020)
Evidence details
Publications
PubMed (9)
Comment:
The p.Arg626X variant in USH2A has been reported >15 individuals with Usher syndrome, at least 9 of whom were homozygous or compound heterozygous with a … (more)
Pathogenic
(Oct 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000959652.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Arg626*) in the USH2A gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Aug 30, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000709899.2
Submitted: (Sep 30, 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
(Jun 19, 2019)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001239876.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
Evidence details
Pathogenic
(Apr 08, 2021)
criteria provided, single submitter
Method: research
Retinitis pigmentosa 39
Allele origin: germline
Ocular Genomics Institute, Massachusetts Eye and Ear
Accession: SCV001573431.1
Submitted: (Apr 26, 2021)
Evidence details
Publications
PubMed (8)
Comment:
The USH2A c.1876C>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Usher syndrome type 2A
Allele origin: germline
Natera, Inc.
Accession: SCV001452253.1
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
An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients. Bonnet C European journal of human genetics : EJHG 2016 PMID: 27460420
Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients. Jiang L Orphanet journal of rare diseases 2015 PMID: 26338283
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
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Seven novel mutations in the long isoform of the USH2A gene in Chinese families with nonsyndromic retinitis pigmentosa and Usher syndrome Type II. Xu W Molecular vision 2011 PMID: 21686329
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
An USH2A founder mutation is the major cause of Usher syndrome type 2 in Canadians of French origin and confirms common roots of Quebecois and Acadians. Ebermann I European journal of human genetics : EJHG 2009 PMID: 18665195
Novel mutations in MYO7A and USH2A in Usher syndrome. Maubaret C Ophthalmic genetics 2005 PMID: 15823922
Comprehensive screening of the USH2A gene in Usher syndrome type II and non-syndromic recessive retinitis pigmentosa. Seyedahmadi BJ Experimental eye research 2004 PMID: 15325563
Mutational spectrum in Usher syndrome type II. Ouyang XM Clinical genetics 2004 PMID: 15025721
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=USH2A - - - -

Text-mined citations for rs534534437...

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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 20, 2021