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NM_206933.3(USH2A):c.3558del (p.Cys1186fs)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Feb 14, 2020
Accession:
VCV000048504.5
Variation ID:
48504
Description:
1bp deletion
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NM_206933.3(USH2A):c.3558del (p.Cys1186fs)

Allele ID
57666
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
1q41
Genomic location
1: 216199880 (GRCh38) GRCh38 UCSC
1: 216373222 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.216199880del
NC_000001.10:g.216373222del
NM_007123.5:c.3558del NP_009054.5:p.Cys1186fs frameshift
... more HGVS
Protein change
C1186fs
Other names
-
Canonical SPDI
NC_000001.11:216199879:A:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA262102
dbSNP: rs397518014
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Dec 16, 2015 RCV000041830.4
Likely pathogenic 1 criteria provided, single submitter Dec 16, 2015 RCV000411413.1
Pathogenic 1 criteria provided, single submitter Sep 17, 2011 RCV000824788.1
Likely pathogenic 1 criteria provided, single submitter May 11, 2019 RCV001073532.1
Pathogenic 1 criteria provided, single submitter Feb 14, 2020 RCV001213213.2
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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
3428 4027
USH2A-AS1 - - - GRCh38 - 334

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 16, 2015)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2A
Allele origin: unknown
Counsyl
Accession: SCV000487464.1
Submitted: (Nov 23, 2016)
Evidence details
Likely pathogenic
(Dec 16, 2015)
criteria provided, single submitter
Method: clinical testing
Retinitis pigmentosa 39
Allele origin: unknown
Counsyl
Accession: SCV000487465.1
Submitted: (Nov 23, 2016)
Evidence details
Pathogenic
(Sep 17, 2011)
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: SCV000065526.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Pathogenic
(Feb 14, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001384834.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Cys1186Trpfs*51) in the USH2A gene. It is expected to result in an absent or disrupted protein … (more)
Likely pathogenic
(May 11, 2019)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001239079.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
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 combination of two truncating mutations in USH2A causes more severe and progressive hearing impairment in Usher syndrome type IIa. Hartel BP Hearing research 2016 PMID: 27318125
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
Frequency of Usher syndrome in two pediatric populations: Implications for genetic screening of deaf and hard of hearing children. Kimberling WJ Genetics in medicine : official journal of the American College of Medical Genetics 2010 PMID: 20613545
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

Text-mined citations for rs397518014...

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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 Jul 07, 2021