NM_181798.1(KCNQ1):c.540+1G>T AND not provided

Clinical significance:Pathogenic (Last evaluated: Jun 21, 2013)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_181798.1(KCNQ1):c.540+1G>T]


KCNQ1:potassium voltage-gated channel subfamily Q member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000011.10:g.2572987G>T
  • NG_008935.1:g.132997G>T
  • NM_000218.2:c.921+1G>T
  • NM_181798.1:c.540+1G>T
  • LRG_287t1:c.921+1G>T
  • LRG_287t2:c.540+1G>T
  • LRG_287:g.132997G>T
  • NC_000011.9:g.2594217G>T
dbSNP: rs397508130
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000218.2:c.921+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_181798.1:c.540+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000234437GeneDxcriteria provided, single submitter
(Jun 21, 2013)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000234437.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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 this study (Splawski I et al., 2000). Additionally, c.921+1 G>T was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This mutation destroys the canonical splice donor site in intron 6 and is predicted to cause abnormal gene splicing. The mutation is predicted to lead to either an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Other splice site mutations in the KCNQ1 gene have been reported in association with LQTS. In summary, c.921+1 G>T in the KCNQ1 gene is interpreted as a disease-causing mutation. The variant is found in LQT panel(s).

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2021

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