NM_181798.1(KCNQ1):c.416T>G (p.Leu139Arg) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Jan 20, 2017)

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.416T>G (p.Leu139Arg)]

NM_181798.1(KCNQ1):c.416T>G (p.Leu139Arg)

KCNQ1:potassium voltage-gated channel subfamily Q member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_181798.1(KCNQ1):c.416T>G (p.Leu139Arg)
  • NC_000011.10:g.2572862T>G
  • NG_008935.1:g.132872T>G
  • NM_000218.2:c.797T>G
  • NM_181798.1:c.416T>G
  • NP_000209.2:p.Leu266Arg
  • NP_861463.1:p.Leu139Arg
  • LRG_287t1:c.797T>G
  • LRG_287t2:c.416T>G
  • LRG_287:g.132872T>G
  • LRG_287p1:p.Leu266Arg
  • LRG_287p2:p.Leu139Arg
  • NC_000011.9:g.2594092T>G
Protein change:
dbSNP: rs199473460
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000218.2:c.797T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181798.1:c.416T>G - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000536354GeneDxcriteria provided, single submitter
Likely pathogenic
(Jan 20, 2017)
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, SCV000536354.4

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


A variant that is likely pathogenic was identified in the KCNQ1 gene. The L266R variant has not been published in association with LQTS to our knowledge. This variant has been reported in one patient with hypertrophic cardiomyopathy (HCM); however, additional clinical information was not provided (Lopes et al., 2015). Nevertheless, the L266R variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; Exome Variant Server). This variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variant in the same residue (L266P) has been reported in the Human Gene Mutation Database in association with LQTS (Stenson et al., 2014), supporting the functional importance of this residue.

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

Last Updated: Oct 8, 2021

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