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NM_000218.3(KCNQ1):c.1022C>T (p.Ala341Val) AND Long QT syndrome 1

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Aug 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000003269.10

Allele description [Variation Report for NM_000218.3(KCNQ1):c.1022C>T (p.Ala341Val)]

NM_000218.3(KCNQ1):c.1022C>T (p.Ala341Val)

Gene:
KCNQ1:potassium voltage-gated channel subfamily Q member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.5
Genomic location:
Preferred name:
NM_000218.3(KCNQ1):c.1022C>T (p.Ala341Val)
Other names:
p.A341V:GCG>GTG
HGVS:
  • NC_000011.10:g.2583535C>T
  • NG_008935.1:g.143545C>T
  • NM_000218.3:c.1022C>TMANE SELECT
  • NM_001406836.1:c.1022C>T
  • NM_001406837.1:c.752C>T
  • NM_001406838.1:c.578C>T
  • NM_181798.2:c.641C>T
  • NP_000209.2:p.Ala341Val
  • NP_000209.2:p.Ala341Val
  • NP_001393765.1:p.Ala341Val
  • NP_001393766.1:p.Ala251Val
  • NP_001393767.1:p.Ala193Val
  • NP_861463.1:p.Ala214Val
  • NP_861463.1:p.Ala214Val
  • LRG_287t1:c.1022C>T
  • LRG_287t2:c.641C>T
  • LRG_287:g.143545C>T
  • LRG_287p1:p.Ala341Val
  • LRG_287p2:p.Ala214Val
  • NC_000011.9:g.2604765C>T
  • NM_000218.2:c.1022C>T
  • NM_181798.1:c.641C>T
  • NR_040711.2:n.915C>T
  • P51787:p.Ala341Val
Protein change:
A193V; ALA341VAL
Links:
UniProtKB: P51787#VAR_001539; OMIM: 607542.0010; dbSNP: rs12720459
NCBI 1000 Genomes Browser:
rs12720459
Molecular consequence:
  • NM_000218.3:c.1022C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406836.1:c.1022C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406837.1:c.752C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406838.1:c.578C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181798.2:c.641C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Long QT syndrome 1 (LQT1)
Identifiers:
MONDO: MONDO:0100316; MedGen: C4551647; Orphanet: 101016; Orphanet: 768; OMIM: 192500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023427OMIM
no assertion criteria provided
Pathogenic
(Oct 25, 2005)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV000805151Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 8, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004024205Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 1, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004047939Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005399414Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 17, 2023)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Evidence of a long QT founder gene with varying phenotypic expression in South African families.

de Jager T, Corbett CH, Badenhorst JC, Brink PA, Corfield VA.

J Med Genet. 1996 Jul;33(7):567-73.

PubMed [citation]
PMID:
8818942
PMCID:
PMC1050664

Positional cloning of a novel potassium channel gene: KVLQT1 mutations cause cardiac arrhythmias.

Wang Q, Curran ME, Splawski I, Burn TC, Millholland JM, VanRaay TJ, Shen J, Timothy KW, Vincent GM, de Jager T, Schwartz PJ, Toubin JA, Moss AJ, Atkinson DL, Landes GM, Connors TD, Keating MT.

Nat Genet. 1996 Jan;12(1):17-23.

PubMed [citation]
PMID:
8528244
See all PubMed Citations (11)

Details of each submission

From OMIM, SCV000023427.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

In 5 kindreds (K1807, K161, K162, K163, and K164) with 47 members affected by LQT1 (192500), Wang et al. (1996) demonstrated a GCG (ala) to GTG (val) transversion in codon 341 of the KVLQT1 gene. The mutation segregated with disease in the families and was not found in DNA samples from 200 unrelated controls.

In affected members of a South African family of Afrikaner origin with LQT (pedigree 166), de Jager et al. (1996) identified heterozygosity for the A341V mutation in the KVLQT1 gene. Haplotype analysis of this family and 4 Afrikaner families previously studied by Wang et al. (1996) (pedigrees 161, 162, 163, and 164) revealed that all 5 families shared a common haplotype, indicating a founder effect. Noting differences in severity of disease between the 2 largest families, 161 and 162, de Jager et al. (1996) suggested that the spectrum of clinical symptoms might reflect the influence of different modulating environmental or genetic backgrounds on expression of the same mutant allele.

Russell et al. (1996) detected this mutation in the spontaneous occurrence of LQT in monozygotic twin offspring of normal parents. This mutation would be expected to encode a potassium channel with altered conductance properties. They noted that mutations at this same nucleotide have been observed in 8 of 19 LQT families determined to have KVLQT1 mutations to that time, suggesting a mutation hotspot. (This variant used to be known as ALA212VAL and ALA246VAL.)

Brink et al. (2005) studied an LQTS founder population (SA-A341V) consisting of 22 apparently unrelated South African kindreds of Afrikaner origin (including pedigrees 161, 162, 163, 164, and 166), all of which could be traced to a single founding couple of mixed Dutch and French Huguenot origin who married in approximately 1730. Comparing the Afrikaner patients to the general LQT1 population, Brink et al. (2005) found that the SA-A341V group exhibited a significantly more severe form of the disease, with an earlier age of onset, longer QTc intervals, and an increased incidence of first cardiac event by age 20 years. Functional analysis in CHO cells demonstrated that coexpression of the A341V mutant reduced the magnitude of wildtype channel repolarizing current by approximately 50%, indicating that the mutation exerts a dominant-negative effect.

Modifier Effects of Variation in the AKAP9 Gene

In 349 members of a South African founder population of Afrikaner origin with LQT1, 168 of whom carried an identical-by-descent A341V mutation, de Villiers et al. (2014) genotyped 4 SNPs in the AKAP9 gene (604001) and found statistically significant associations between certain alleles, genotypes, and haplotypes and phenotypic traits such as QTc interval length, risk of cardiac events, and/or disease severity. De Villiers et al. (2014) stated that these results clearly demonstrated that AKAP9 contributes to LQTS phenotypic variability; however, the authors noted that because these SNPs are located in intronic regions of the gene, functional or regulatory variants in linkage disequilibrium with the SNPs were likely to be responsible for the modifying effects.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues, SCV000805151.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes, SCV004024205.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047939.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.1022C>T (p.Ala341Val) missense variant in KCNQ1 gene has been reported in individuals affected with long QT syndrome (Brink et al., 2005). This variant has been observed to segregate with long QT syndrome (LQTS) in several families (Brink et al., 2005). Experimental studies have shown that this missense change reduces the current of the KCNQ1 channel in a dominant negative fashion (Brink et al., 2005). This variant disrupts the p.Ala341 amino acid residue in KCNQ1. Other variant(s) that disrupt this residue have been observed in affected individuals (Anastasakis et al., 2006), suggesting that it is a clinically significant residue. The p.Ala341Val variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The amino acid Ala at position 341 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ala341Val in KCNQ1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005399414.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative, loss of function and gain of function are known mechanisms of disease in this gene. Gain of function variants result exclusively in short QT syndrome (MIM#609621), while dominant negative and loss of function variants can cause long QT syndrome (LQTS, MIM#192500), atrial fibrillation (MIM#607554) and Jervell and Lange-Nielsen syndrome (JLNS, MIM#220400) (OMIM, PMIDs: 19632626, 28438721). (I) 0108 - This gene is known to be associated with both recessive and dominant disease. JLNS is characterized by congenital, bilateral deafness and variable degrees of QT prolongation, and is the only condition caused by biallelic variants (PMID: 28438721). (I) 0112 - The condition associated with this gene has incomplete penetrance (OMIM, PMID: 20301308). (I) 0200 - Variant is predicted to result in a missense amino acid change from alanine to valine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated S6 transmembrane domain (PMID: 19716085). (I) 0702 - Other missense variants comparable to the one identified in this case have strong previous evidence for pathogenicity. An alternative change to a glutamic acid and a glycine have been reported in multiple individuals with LQTS (ClinVar, PMID: 19716085). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as a South African founder mutation and has multiple pathogenic entries in ClinVar (PMID: 24217263, 19716085). (SP) 1204 - This variant has been shown to be de novo in the proband (parental status not tested but assumed). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Feb 25, 2025