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NM_181798.1(KCNQ1):c.540+1G>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 30, 2020
Accession:
VCV000053126.3
Variation ID:
53126
Description:
single nucleotide variant
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NM_181798.1(KCNQ1):c.540+1G>T

Allele ID
67794
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 2572987 (GRCh38) GRCh38 UCSC
11: 2594217 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_287t2:c.540+1G>T
LRG_287:g.132997G>T
LRG_287t1:c.921+1G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:2572986:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA008659
dbSNP: rs397508130
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Jun 21, 2013 RCV000182134.2
Likely pathogenic 1 criteria provided, single submitter Sep 30, 2020 RCV001377884.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
KCNQ1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
1161 1427

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 21, 2013)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000234437.9
Submitted: (Jul 13, 2017)
Evidence details
Comment:
The c.921+1 G>T mutation has been reported previously in one individual referred for LQTS testing, and was absent from at least 400 control chromosomes in … (more)
Likely pathogenic
(Sep 30, 2020)
criteria provided, single submitter
Method: clinical testing
Long QT syndrome
Allele origin: germline
Invitae
Accession: SCV001575331.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 6 of the KCNQ1 gene. It is expected to disrupt RNA splicing and likely results … (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
The genetic basis of long QT and short QT syndromes: a mutation update. Hedley PL Human mutation 2009 PMID: 19862833
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Spectrum of mutations in long-QT syndrome genes. KVLQT1, HERG, SCN5A, KCNE1, and KCNE2. Splawski I Circulation 2000 PMID: 10973849
Dominant-negative KvLQT1 mutations underlie the LQT1 form of long QT syndrome. Shalaby FY Circulation 1997 PMID: 9323054

Text-mined citations for rs397508130...

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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 Oct 08, 2021