rs199473671

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000218.3(KCNQ1):c.136G>A(p.Ala46Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000673 in 1,143,396 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.000074 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000066 ( 0 hom. )

Consequence

KCNQ1
NM_000218.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:9O:1

Conservation

PhyloP100: 0.596

Variant links:

Genes affected

KCNQ1 (HGNC:6294): (potassium voltage-gated channel subfamily Q member 1) This gene encodes a voltage-gated potassium channel required for repolarization phase of the cardiac action potential. This protein can form heteromultimers with two other potassium channel proteins, KCNE1 and KCNE3. Mutations in this gene are associated with hereditary long QT syndrome 1 (also known as Romano-Ward syndrome), Jervell and Lange-Nielsen syndrome, and familial atrial fibrillation. This gene exhibits tissue-specific imprinting, with preferential expression from the maternal allele in some tissues, and biallelic expression in others. This gene is located in a region of chromosome 11 amongst other imprinted genes that are associated with Beckwith-Wiedemann syndrome (BWS), and itself has been shown to be disrupted by chromosomal rearrangements in patients with BWS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]

KCNQ1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNQ1	NM_000218.3 link	c.136G>A	p.Ala46Thr	missense_variant	Exon 1 of 16	ENST00000155840.12	NP_000209.2	P51787-1Q96AI9
KCNQ1	NM_001406836.1 link	c.136G>A	p.Ala46Thr	missense_variant	Exon 1 of 15		NP_001393765.1
KCNQ1	NM_001406838.1 link	c.136G>A	p.Ala46Thr	missense_variant	Exon 1 of 11		NP_001393767.1
KCNQ1	NM_001406837.1 link	c.-227G>A		5_prime_UTR_variant	Exon 1 of 17		NP_001393766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
KCNQ1	ENST00000155840.12 link	c.136G>A	p.Ala46Thr	missense_variant	Exon 1 of 16	1	NM_000218.3	ENSP00000155840.2	P51787-1
KCNQ1	ENST00000646564.2 link	c.136G>A	p.Ala46Thr	missense_variant	Exon 1 of 11			ENSP00000495806.2	A0A2R8YEQ9
KCNQ1	ENST00000496887.7 link	c.24-149G>A		intron_variant	Intron 1 of 15	5		ENSP00000434560.2	E9PPZ0
KCNQ1	ENST00000345015.4 link	n.-88G>A		upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0000742

AC:

AN:

148180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000165

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000600

AC:

AN:

16670

Hom.:

AF XY:

0.00

AC XY:

AN XY:

10080

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000163

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000663

AC:

AN:

995216

Hom.:

Cov.:

AF XY:

0.0000588

AC XY:

AN XY:

476588

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000741

Gnomad4 OTH exome

AF:

0.0000277

GnomAD4 genome

AF:

0.0000742

AC:

AN:

148180

Hom.:

Cov.:

AF XY:

0.0000416

AC XY:

AN XY:

72154

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000165

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000945

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:9Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:4

Aug 24, 2021

AiLife Diagnostics, AiLife Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 30, 2025

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed in multiple individuals referred for long QT syndrome genetic testing in the literature (Napolitano et al., 2005; Chung et al., 2007; Kapplinger et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21118729, 19716085, Pelletti2020[abstract], 16414944, 24144883, 25786344, 17905336, 25119684, 23631430, 28595573, 19808498, 32048431, 31737537, 30847666, 33600800, 34505893, 26423924, 23130128, 39244732) -

Apr 24, 2023

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_SUP -

Nov 13, 2017

Stanford Center for Inherited Cardiovascular Disease, Stanford University

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: provider interpretation

KCNQ1 p.Ala46Thr (c.136 G>A) Case data: The variant has been seen in: -2 case of LQTS -2-3 cases of possible LQTS â€“ 1 in our center, 1-2 from the Familion cohort -1 case of syncope and QT-prolongation in the setting of a QT-prolonging medication with a family history of young sudden death and syncope. Other relatives with syncope did not have prolonged QT intervals and the variant did not segregate with syncope in the family. -1 case of early-onset atrial fibrillation with non-sustained ventricular tachycardia, inducible polymorphic and monomorphic ventricular tachycardia and an ejection fraction of 50% -1 case of focal epilepsy with a personal or family history of SUDEP. Long QT cases: Napolitano et al (2005) reported the variant in a list of novel variants observed in their Italian cohort of long QT syndrome patients. Robyn Hylind shared that they have seen this variant in a patient with LQTS in their center (children's hospital boston). The patient was also worked up at CHOP and Yale and had clinical genetic testing so there may be redundancy with other cases (I counted this case in the summary above and reduced the Familion count, suspecting the patient was tested there). The proband presented at 5yo with recurrent syncope, QTc 500 ms, QTc 550 ms on exercise testing. Brother is a carrier and has a QTc of 380 ms. Borderline or other phenotypes: Chung et al (2007) observed the variant in one individual with syncope, a prolonged QTc (in the setting of Cisapride, which is QT-prolonging), and a family history of sudden death in their cohort from New Zealand. The same group later published what appears to be additional data on the same patient that may be suggestive of failure to segregate or perhaps even that long QT is not the right phenotype (Yang et al 209). Two other family members have the variant, a history of syncope, and maximal QTc intervals of 440 ms (in a female) and 420 ms (in a male). Another family member has a history of syncope and a maximal QTc of 440 ms but doesn't have the variant. The authors note they are not using the variant for cascade screening. I suspect the same family is reported in Rice et al (2011). I connect with Dr. Jon Skinner, who leads this group. He re-reviewed the case and noted he thinks it is most likely a VUS and that the original exercise data supporting long QT is perhaps not very strong and may in fact be normal. The variant was observed in two different patients in the Familion/PGxHealth published cohort (Kapplinger et al 2009), which includes 2500 patients referred for clinical long QT genetic testing. Those cases likely overlap with the data in Kapa et al (2009) and Giudicessi et al (2012) since these are all from Ackerman's group and use data from his cohort and from the Familion cohort. Of note in considering the cases reported by Kapplinger et al (2009) is the lack of phenotypic data on this cohort, the low yield of 36% (vs. 70% in cohorts with firm diagnoses of long QT), and the lack of clarity regarding which variants were seen with another variant (9% of the cohort had multiple variants). These cases are likely redundant with Aziz et al (2011) as they report doing testing through Familion/PGxHealth. They do not provide any additional phenotypic detail and the inclusion criteria for the study did not include clearly abnormal QT length. Steffensen et al (2015) report the variant in an individual with atrial fibrillation onset at 38yo, a normal QTc (428 ms), and non-sustained ventricular tachycardia, recruited in Denmark (presumably redundant with Olesen et al 2014 and meeting abstract by Olesen et al). Work-up was extensive including coronary angiography, cardiac MRI, echocardiogram, stress test, and myocardial biopsy. Echo showed ejection fraction of 50% with no other abnormalities found. On EP study there was inducible polymorphic ventricular tachycardia, monomorphic ventricular tachycardia, and atrial fibrillation. An ICD was placed but had not discharged by -

Long QT syndrome 1

Uncertain:1

Feb 23, 2018

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Uncertain:1

Aug 06, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Ala46Thr variant in KCNQ1 has not been previously reported in individuals with hearing loss or Jervell and Lange-Nielsen syndrome, but has been identified in 1 individual with early onset (<40 years) atrial fibrillation (Olesen 2014), in 1 individual with focal epilepsy (Partemi 2015), in 2 individuals with long QT syndrome (Kaplinger 2009), and in 1 individual with suspected LQTS and syncop e (Chung 2007, Yang 2009). However, the individual with suspected LQTS and synco pe had 3 relatives with syncope without LQTS, and only 2 of 3 of these relatives carried the variant (Yang 2009). This variant was absent in 3500 control chromo somes reported in three studies (Napolitano 2005, Chung 2007, Kapplinger 2009) a nd absent from the gnomAD database. In-vitro functional studies provided inconcl usive evidence on the impact of this variant on normal protein function (Yang 20 09). In addition, alanine (Ala) at position 46 is not conserved through species, with 1 mammal (rat) having a threonine (Thr) at this position, suggesting that variants at this position may be tolerated. In summary, due to conflicting data, the clinical significance of the p.Ala46Thr variant is uncertain. -

Beckwith-Wiedemann syndrome;C1837014:Atrial fibrillation, familial, 3;C1865019:Short QT syndrome type 2;C4551509:Jervell and Lange-Nielsen syndrome 1;C4551647:Long QT syndrome 1

Uncertain:1

Oct 31, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Long QT syndrome

Uncertain:1

Jan 28, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 46 of the KCNQ1 protein (p.Ala46Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with lone atrial fibrillation and/or long QT syndrome (PMID: 16414944, 17905336, 19808498, 21118729, 23130128, 24144883, 25786344, 30847666, 31737537, 34505893). ClinVar contains an entry for this variant (Variation ID: 52982). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt KCNQ1 protein function with a negative predictive value of 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on KCNQ1 function (PMID: 19808498, 33600800). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Cardiovascular phenotype

Uncertain:1

Jul 29, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.136G>A (p.A46T) alteration is located in exon 1 (coding exon 1) of the KCNQ1 gene. This alteration results from a G to A substitution at nucleotide position 136, causing the alanine (A) at amino acid position 46 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Congenital long QT syndrome

Other:1

Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:16414944;PMID:17905336;PMID:19716085;PMID:19808498). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Pathogenic

0.19

BayesDel_noAF

Uncertain

0.040

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.29

Eigen

Benign

-0.73

Eigen_PC

Benign

-0.64

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.41

M_CAP

Pathogenic

0.96

MetaRNN

Uncertain

0.59

MetaSVM

Uncertain

0.38

MutationAssessor

Benign

0.55

PrimateAI

Pathogenic

0.88

PROVEAN

Benign

-0.20

REVEL

Uncertain

0.52

Sift

Benign

0.28

Sift4G

Benign

0.58

Polyphen

0.0

Vest4

0.67

MVP

0.88

MPC

1.1

ClinPred

0.055

GERP RS

1.4

Varity_R

0.035

gMVP

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over