11-2583457-A-G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000218.3(KCNQ1):c.944A>G(p.Tyr315Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y315H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: KCNQ1 NM_000218.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8 O:1
• Conservation: PhyloP100: 8.73

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 15 uncertain in NM_000218.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-2583456-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 449302.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.994
• PP5: Variant 11-2583457-A-G is Pathogenic according to our data. Variant chr11-2583457-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 53140.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-2583457-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNQ1	NM_000218.3	c.944A>G	p.Tyr315Cys	missense_variant	7/16	ENST00000155840.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ1	ENST00000155840.12	c.944A>G	p.Tyr315Cys	missense_variant	7/16	1	NM_000218.3	P1
KCNQ1	ENST00000335475.6	c.563A>G	p.Tyr188Cys	missense_variant	7/16	1
KCNQ1	ENST00000496887.7	c.683A>G	p.Tyr228Cys	missense_variant	8/16	5
KCNQ1	ENST00000646564.2	c.500A>G	p.Tyr167Cys	missense_variant	3/11

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461218 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726932

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 02, 2016	p.Tyr315Cys (c.944A>G, p.Y315C) in the KCNQ1 gene The variant was re-reviewed March 2nd, 2016. There was both new case data and new allele frequency data, both of which further support pathogenicity and shift our classification from likely pathogenic to pathogenic. The variant has been seen in at least 13 unrelated cases of long QT syndrome (not including this patient). We seen this variant in one other family with long QT in our center. Splawski et al (1998) reported this variant in a patient with long QT syndrome, presumably from their American cohort (ancestry not noted). Priori et al (1999) reported the variant in a patient from their Italian cohort with long QT syndrome. Chen et al (2003) observed the variant in two siblings with long QT syndrome (cohort studied at Cleveland clinic, recruited from clinics in North America, South America, Europe; ancestry not provided). Choi et al (2004) reported the variant in an "LQT1 index case" (no other phenotypic data provided) who had a cousin with exertional syncope and a near-drowning event (cohort studied in Dr. Ackerman's lab at Mayo; ancestry not provided). This case likely overlaps with Nemec et al (2003) and Tester et al (2005), also from Dr. Ackerman's group. The variant was observed in 4 patients included in the Familion compendium publication with no phenotype or ancestry data (Kapplinger et al 2009). This publication reports on variants observed in patients referred for long QT syndrome genetic testing using the Familion test at PGxHealth (now Transgenomics). Napolitano et al (2000) reported the variant in a woman with QT-prolongation and arrest in the setting of a QT-prolonging medication (cisapride) (ancestry not noted but patient likely from Italy). Patients with this variant are included in two papers on genotype-phenotype correlations (Zareba et al 2003, Moss et al 2007). The subjects were drawn from the various long QT registries and many of the authors overlap with the other publications reviewed here, so at least some of the cases are likely redundant with those summarized above. Stattin et al (2012) studied 200 unrelated index cases of LQTS referred for care in Sweden between 3/2006 and 10/2009. KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A were analyzed. The variant of interest was found in a single proband; no segregation data is reported. Hedley et al (2013) studied 44 South African congenital LQTS patients, screening them for variants in the coding regions of KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A. The variant of interest was found in one patient (no segregation data reported). Christiansen et al (2014) assessed 70 unrelated Danish LQTS probands by variant screening of KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A. The variant of interest was found in a single proband; no segregation data is reported. In silico analysis with PolyPhen-2 predicts the variant to be probably damaging. Grantham score is 5.29. The tyrosine at codon 315 is completely conserved across species, as are neighboring amino acids. Other variants have been reported in association with disease at this codon (p.Tyr315Ser, p.Tyr315Phe) and nearby codons (p.Ile313Met, p.Gly314Asp, p.Gly314Ala, p.Gly314Ser, p.Gly314Cys, p.Gly314Arg, p.Gly314Val, p.GLy316Glu, p.GLy316Arg). Functional studies have shown a decrease in potassium current (Bianchi et al 2000). The variant is in the pore region of the channel. Variants in this region are much more likely to be pathogenic than benign. There is also some evidence that they confer a higher risk of events (Moss et al 2007), though other studies have not found such a difference (Zareba et al 2003). Barsheshet et al (2012) found that carriers of missense variants in the cytoplasmic loops had the highest risk of events as well as the greatest response to beta-blockade. The patient's variant is not in the cytoplasmic loop. Moss et al (2007) reported a higher risk with dominant negative variants and classify this variant as dominant negative. In total the variant has no -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2022	Published functional studies demonstrate a damaging effect as this variant results in reduced potassium channel current in vitro (Bianchi et al., 2000); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15466642, 24269949, 19490272, 14678125, 9693036, 9927399, 17470695, 15840476, 19261104, 23575362, 23130128, 12877697, 12702160, 24606995, 18774102, 23098067, 19716085, 24217263, 28749187, 27920829, 28438721, 10868744, 14760488, 20541041, 10220144, 31447099, 34135346, 11087258) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2022	KCNQ1: PM1, PM2, PM5, PS4:Moderate, PP3, PS3:Supporting -

Long QT syndrome 1 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Nov 03, 2017	The c.944A>G (p.Tyr315Cys) variant in the KCNQ1 gene has been observed in multiple individuals with long QT syndrome (PMID: 9693036, 10868744, 12702160, 15840476, 14760488, 15466642). In addition, experimental studies have shown that this missense change leads to altered KCNQ1 protein function (PMID: 11087258). The c.944A>G (p.Tyr315Cys) variant in the KCNQ1 gene is classified as likely pathogenic. -
Likely pathogenic, no assertion criteria provided	research	deCODE genetics, Amgen	Jul 21, 2023	The variant NM_000218.3:c.944A>G (chr11:2583457) in KCNQ1 was detected in 17 heterozygotes out of 58K WGS Icelanders (MAF= 0,015%). Following imputation in a set of 166K Icelanders (48 imputed heterozygotes) we observed an association with an elongation of the qt interval on ECG using measurements from 80068 individuals (Effect (SD)= 2.21, P= 5.38e-26) and heart failure using 20765 cases and 367806 controls (OR= 3.17, P= 1.31e-02). This variant has been reported in ClinVar previously as pathogenic/likely pathogenic. Based on ACMG criteria (PS4, PM1, PP3, PP5) this variant classifies as likely pathogenic. -

Long QT syndrome Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	Jan 18, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 29, 2023	This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 315 of the KCNQ1 protein (p.Tyr315Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 9693036, 12702160, 18774102, 21451124, 24217263, 24606995). ClinVar contains an entry for this variant (Variation ID: 53140). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KCNQ1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 11087258, 21451124). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 01, 2023

The p.Y315C pathogenic mutation (also known as c.944A>G), located in coding exon 7 of the KCNQ1 gene, results from an A to G substitution at nucleotide position 944. The tyrosine at codon 315 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration impacts the highly conserved ion selectivity filter (TIGYGD) located between transmembrane helices S5 and S6. This alteration has been detected in multiple unrelated individuals reported to have confirmed or suspected long QT syndrome, with variable expressivity in some cases (LQTS) (Splawski I et al. Genomics. 1998;51(1):86-97; Chen S et al. Clin Genet. 2003;63(4):273-82; Moss AJ et al. Circulation. 2007; Kapplinger JD et al. Heart Rhythm. 2009;6(9):1297-303; 115(19):2481-9; Itoh H et al. Heart Rhythm. 2010;7(10):1411-8; Bartos DC et al. Heart Rhythm. 2014;11(3):459-68). One study reported this alteration to result in a dominant negative effect on wild-type IKs current when expressed with wild-type channel in vitro (Bianchi L et al. Am J Physiol Heart Circ Physiol. 2000;279(6):H3003-11). Internal structural analysis indicates that this variant disrupts the ion channel pore and is expected to eliminate the K+ selectivity of the K+ channel (Tao X et al. Science. 2009;326(5960):1668-74; Whorton MR and MacKinnon R. Cell. 2011;147(1):199-208; Ambry internal data). In addition, another alteration affecting this codon (p.Y315S, c.944A>C) has also been reported in association with LQTS (Jongbloed RJ et al. Hum Mutat. 1999;13(4):301-10). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Congenital long QT syndrome Other:1

not provided, no classification provided

literature only

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

-

This variant has been reported as associated with Long QT syndrome in the following publications (PMID:9693036;PMID:10868744;PMID:12702160;PMID:12877697;PMID:14678125;PMID:14760488;PMID:15466642;PMID:15840476;PMID:19716085;PMID:9927399;PMID:17470695). 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	Pathogenic	0.99
CardioboostArm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.60
Cadd	Pathogenic	28
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	D;.;.
Eigen	Pathogenic	0.81
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Pathogenic	0.98	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	H;.;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-8.4	D;.;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;.;D
Sift4G	Pathogenic	0.0	D;.;D
Polyphen		1.0	D;.;D
Vest4		0.99
MutPred		0.94		Loss of helix (P = 0.0558);.;.;
MVP		0.99
MPC		1.3
ClinPred		1.0	D
GERP RS		3.9
Varity_R		0.97
gMVP		0.99

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

Other links and lift over

dbSNP: rs74462309; hg19: chr11-2604687; COSMIC: COSV50102637;