rs199472751

Positions:

• chr11-2583462-G-A
• chr11-2583462-G-T

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.949G>A​(p.Asp317Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D317G) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KCNQ1 NM_000218.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3 O:1
• Conservation: PhyloP100: 9.36

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 intramembrane_region Pore-forming; Name=Segment H5 (size 20) in uniprot entity KCNQ1_HUMAN there are 54 pathogenic changes around while only 0 benign (100%) 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 chr11-2583463-A-G is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.991
• PP5: Variant 11-2583462-G-A is Pathogenic according to our data. Variant chr11-2583462-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 53145.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-2583462-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNQ1	NM_000218.3	c.949G>A	p.Asp317Asn	missense_variant	7/16	ENST00000155840.12	NP_000209.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNQ1	ENST00000155840.12	c.949G>A	p.Asp317Asn	missense_variant	7/16	1	NM_000218.3	ENSP00000155840.2
KCNQ1	ENST00000335475.6	c.568G>A	p.Asp190Asn	missense_variant	7/16	1		ENSP00000334497.5
KCNQ1	ENST00000496887.7	c.688G>A	p.Asp230Asn	missense_variant	8/16	5		ENSP00000434560.2
KCNQ1	ENST00000646564.2	c.505G>A	p.Asp169Asn	missense_variant	3/11			ENSP00000495806.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Apr 23, 2018

This missense change is denoted Asp317Asn (aka D317N) at the protein level and c.949 G>A at the cDNA level. The Asp317Asn mutation (also reported as Asp222Asn and Asp188Asn due to alternative nomenclature) in KCNQ1 has been reported previously in multiple individuals with LQTS, and has been shown to co-segregate with an LQTS phenotype in at least two large families (Wollnick B et al.,1997, Saarinen K et al., 1998, Chen S et al., 2003 ). Swan et al. (1999) reported the QT prolongation is exacerbated during exercise and recovery in individuals harboring the Asp317Asn mutation, consistent with the development of symptoms during exercise for several of the patients reported (Saarinen K et al., 1998, Chen S et al., 2003, Swan H et al., 1999). Considering all publications, the Asp317Asn mutation was absent from 550 control alleles (Wollnick B et al.,1997, Saarinen K et al., 1998, Swan H et al., 1999). The Asp317Asn mutation was not identified in 400 Caucasian and African American control chromosomes tested at GeneDx, and the NHLBI ESP Exome Variant Server reports Asp317Asn was not observed in approximately 5,000 samples from individuals of European and African American backgrounds, indicating it is not a common benign variant in these populations. The Asp317Asn mutation affects the pore region of the cardiac potassium voltage-gated channel, KQT-like type 1, an important functional region of the protein (Wollnick B et al.,1997). Furthermore, mutations at the same codon (Asp317Gly, Asp317Tyr) as well as in neighboring codons (Gly316Arg, Gly316Glu, Gly316Val, Lys318Asn) have also been reported in association with LQTS, further supporting the functional importance of this region of the protein. The variant is found in LQT panel(s). -

Long QT syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 07, 2023

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 317 of the KCNQ1 protein (p.Asp317Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 9302275, 9482580, 10973849, 11410559, 12702160, 23631430, 26063740). It has also been observed to segregate with disease in related individuals. This variant is also known as p.Asp222Asn, p.Asp188Asn. ClinVar contains an entry for this variant (Variation ID: 53145). 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: 9302275, 25705178). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 27, 2017

Variant summary: The KCNQ1 c.949G>A (p.Asp317Asn) variant involves the alteration of a conserved nucleotide located in the Ion transport domain (InterPro), and in the H5 loop, which is an important part of the pore (Wollnik_1997). 4/5 in silico tools predict a damaging outcome for this variant. This variant is absent in 121152 control chromosomes. The variant has been reported in the literature to perfectly segregate with LQTS in at least two families (Wollnik_1997, Chen_2003), and was reported in a patient group which displayed the longest QT intervals as well as the most impaired heart rate responses to exercise compared to patient groups with other types of mutations in KCNQ1 (Swan_1999). Functional studies show the variant to abolish channel activity and reduce the activity of wild-type KvLQT1 by a dominant negative mechanism (Wollnik_1997). In addition, at-least one clinical diagnostic laboratory in ClinVar database has classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. -

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:9302275;PMID:9482580;PMID:12702160). 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	0.93
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.19
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	D;.;.
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Pathogenic	0.92	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M;.;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Pathogenic	-4.7	D;.;D
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D;.;D
Sift4G	Uncertain	0.0050	D;.;D
Polyphen		1.0	D;.;D
Vest4		0.99
MutPred		0.94		Gain of sheet (P = 0.0477);.;.;
MVP		0.98
MPC		1.2
ClinPred		1.0	D
GERP RS		3.9
Varity_R		0.93
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: rs199472751; hg19: chr11-2604692;