chr11-2445430-A-G

Variant names:

• chr11-2445430-A-G
• rs199472678
• NM_000218.3:c.332A>G

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PS3 PM2 PP3_Strong PP5_Very_Strong

The NM_001406837.1(KCNQ1):​c.-31A>G variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000346 in 1,445,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). ClinVar reports functional evidence for this variant: "SCV000234563: Functional studies have demonstrated that Y111C, which is located in the N-terminal region of the protein, alters a motif that plays a key role in intracellular trafficking of the potassium channel, thus trapping the protein in the endoplasmic reticulum and rendering the channels inactive (Dahimene et al., 2006; Peroz et al., 2009, Winbo et al., 2009; Lee et al., 2020);; SCV000280152: Dahieme et al (2006) did show that cardiomyocites with the variant have impaired protein trafficking and malfunctioning potassium channel subunits. PMID:16825087; SCV002606259: Functional studies have demonstrated that this mutation results in no cell surface expression or potassium current, with the protein retained in the endoplasmic reticulum (Peroz D et al. J. Biol. Chem., 2009 Feb;284:5250-6; Dahimène S et al. Circ. Res., 2006 Nov;99:1076-83).; SCV003439745: Experimental studies have shown that this missense change affects KCNQ1 function (PMID:17053194, 19114714, 29532034).; SCV005400411: "This variant has moderate functional evidence supporting abnormal protein function. In vitro analysis demonstrates this variant exerts a dominant negative effect that results in a channel trafficking defect (PMID:17053194)."".

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: KCNQ1 NM_001406837.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 6.18
• Publications: 44 publications found

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 Gene-Disease associations (from GenCC):

• long QT syndrome

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• long QT syndrome 1

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• Jervell and Lange-Nielsen syndrome

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• Jervell and Lange-Nielsen syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• atrial fibrillation, familial, 3

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• short QT syndrome

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet
• short QT syndrome type 2

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• familial atrial fibrillation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Jervell and Lange-Nielsen syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hypertrophic cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000234563: Functional studies have demonstrated that Y111C, which is located in the N-terminal region of the protein, alters a motif that plays a key role in intracellular trafficking of the potassium channel, thus trapping the protein in the endoplasmic reticulum and rendering the channels inactive (Dahimene et al., 2006; Peroz et al., 2009, Winbo et al., 2009; Lee et al., 2020);; SCV000280152: Dahieme et al (2006) did show that cardiomyocites with the variant have impaired protein trafficking and malfunctioning potassium channel subunits. PMID:16825087; SCV002606259: Functional studies have demonstrated that this mutation results in no cell surface expression or potassium current, with the protein retained in the endoplasmic reticulum (Peroz D et al. J. Biol. Chem., 2009 Feb;284:5250-6; Dahimène S et al. Circ. Res., 2006 Nov;99:1076-83).; SCV003439745: Experimental studies have shown that this missense change affects KCNQ1 function (PMID: 17053194, 19114714, 29532034).; SCV005400411: "This variant has moderate functional evidence supporting abnormal protein function. In vitro analysis demonstrates this variant exerts a dominant negative effect that results in a channel trafficking defect (PMID:17053194)."
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982
• PP5: Variant 11-2445430-A-G is Pathogenic according to our data. Variant chr11-2445430-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 53035.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001406837.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ1	NM_000218.3	MANE Select	c.332A>G	p.Tyr111Cys	missense	Exon 1 of 16	NP_000209.2
	KCNQ1	NM_001406837.1		c.-31A>G		5_prime_UTR_premature_start_codon_gain	Exon 1 of 17	NP_001393766.1
	KCNQ1	NM_001406836.1		c.332A>G	p.Tyr111Cys	missense	Exon 1 of 15	NP_001393765.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNQ1	ENST00000155840.12	TSL:1 MANE Select	c.332A>G	p.Tyr111Cys	missense	Exon 1 of 16	ENSP00000155840.2	P51787-1
	KCNQ1	ENST00000345015.4	TSL:1	n.109A>G		non_coding_transcript_exon	Exon 1 of 3
	KCNQ1	ENST00000910997.1		c.332A>G	p.Tyr111Cys	missense	Exon 1 of 16	ENSP00000581056.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000894 AC: 2 AN: 223694 AF XY: 0.0000161

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 FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000199

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000346 AC: 5 AN: 1445536 Hom.: 0 Cov.: 31 AF XY: 0.00000556 AC XY: 4 AN XY: 719524

African (AFR) AF: 0.00 AC: 0 AN: 33466

American (AMR) AF: 0.00 AC: 0 AN: 44666

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26104

East Asian (EAS) AF: 0.00 AC: 0 AN: 39672

South Asian (SAS) AF: 0.00 AC: 0 AN: 86122

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37802

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5754

European-Non Finnish (NFE) AF: 0.00000360 AC: 4 AN: 1111710

Other (OTH) AF: 0.0000166 AC: 1 AN: 60240

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000432 Hom.: 0

ExAC AF: 0.0000168 AC: 2

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
3	-	-	not provided (3)
2	-	-	Cardiovascular phenotype (2)
1	-	-	Long QT syndrome (1)
1	-	-	Long QT syndrome 1 (1)
-	-	-	Congenital long QT syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
CardioboostArm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.86	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Benign	2.0	M
PhyloP100		6.2
PrimateAI	Pathogenic	0.91	D
PROVEAN	Pathogenic	-6.3	D
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.96
MutPred		0.89		Gain of helix (P = 0.0696)
MVP		0.99
MPC		2.5
ClinPred		0.99	D
GERP RS		3.0
PromoterAI		-0.036	Neutral
Varity_R		0.97
gMVP		0.99
Mutation Taster		=1/99	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs199472678; hg19: chr11-2466660;