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NM_000238.4(KCNH2):c.1790A>G (p.Tyr597Cys)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Dec 21, 2016)
Last evaluated:
Nov 18, 2015
Accession:
VCV000067277.1
Variation ID:
67277
Description:
single nucleotide variant
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NM_000238.4(KCNH2):c.1790A>G (p.Tyr597Cys)

Allele ID
78173
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q36.1
Genomic location
7: 150951603 (GRCh38) GRCh38 UCSC
7: 150648691 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000238.3:c.1790A>G NP_000229.1:p.Tyr597Cys missense
Q12809:p.Tyr597Cys
LRG_288t1:c.1790A>G LRG_288p1:p.Tyr597Cys
... more HGVS
Protein change
Y257C, Y597C
Other names
-
Canonical SPDI
NC_000007.14:150951602:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs199472934
ClinGen: CA005509
UniProtKB: Q12809#VAR_074841
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 Nov 18, 2015 RCV000168208.2
Likely pathogenic 1 criteria provided, single submitter Nov 12, 2015 RCV000414552.1
not provided 1 no assertion provided - RCV000057993.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNH2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2038 2109

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Nov 18, 2015)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome
Allele origin: germline
Invitae
Accession: SCV000218873.4
Submitted: (Jun 10, 2016)
Evidence details
Comment:
This sequence change replaces tyrosine with cystine at codon 597 of the KCNH2 protein (p.Tyr597Cys). The tyrosine residue is highly conserved and there is a … (more)
Likely pathogenic
(Nov 12, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000490927.1
Submitted: (Dec 21, 2016)
Evidence details
Comment:
The Y597C likely pathogenic variant in the KCNH2 gene has been reported previously in one individual referred for LQTS genetic testing, and was absent from … (more)
not provided
(-)
no assertion provided
Method: literature only
Congenital long QT syndrome
Allele origin: germline
Cardiovascular Biomedical Research Unit,Royal Brompton & Harefield NHS Foundation Trust
Accession: SCV000089513.3
Submitted: (Sep 22, 2016)
Evidence details
Publications
PubMed (2)
Comment:
This variant has been reported as associated with Long QT syndrome in the following publications (PMID:19716085). This is a literature report, and does not necessarily … (more)

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
Paralogous annotation of disease-causing variants in long QT syndrome genes. Ware JS Human mutation 2012 PMID: 22581653
Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Kapplinger JD Heart rhythm 2009 PMID: 19716085

Text-mined citations for rs199472934...

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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