rs199472947

Positions:

• chr7-150951540-G-A
• chr7-150951540-G-C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000238.4(KCNH2):​c.1853C>T​(p.Thr618Ile) 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. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: KCNH2 NM_000238.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2 O:1
• Conservation: PhyloP100: 9.85

Genes affected

KCNH2 (HGNC:6251): (potassium voltage-gated channel subfamily H member 2) This gene encodes a component of a voltage-activated potassium channel found in cardiac muscle, nerve cells, and microglia. Four copies of this protein interact with one copy of the KCNE2 protein to form a functional potassium channel. Mutations in this gene can cause long QT syndrome type 2 (LQT2). Transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, May 2022]

KCNH2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a intramembrane_region Pore-forming; Name=Segment H5 (size 20) in uniprot entity KCNH2_HUMAN there are 23 pathogenic changes around while only 0 benign (100%) in NM_000238.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.945
• PP5: Variant 7-150951540-G-A is Pathogenic according to our data. Variant chr7-150951540-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 67297.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNH2	NM_000238.4	c.1853C>T	p.Thr618Ile	missense_variant	7/15	ENST00000262186.10	NP_000229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNH2	ENST00000262186.10	c.1853C>T	p.Thr618Ile	missense_variant	7/15	1	NM_000238.4	ENSP00000262186.5

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Long QT syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 27, 2023

This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 618 of the KCNH2 protein (p.Thr618Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with short QT syndrome (PMID: 21130771; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 67297). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects KCNH2 function (PMID: 21130771, 23300672, 23471968). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 01, 2017

The p.T618I pathogenic mutation (also known as c.1853C>T), located in coding exon 7 of the KCNH2 gene, results from a C to T substitution at nucleotide position 1853. The threonine at codon 618 is replaced by isoleucine, an amino acid with similar properties. This alteration has been reported in multiple cases of short QT syndrome (SQTS) and has segregated with SQTS in multiple families, many of which had significant histories of arrhythmia and sudden death (Sun Y et al. J Mol Cell Cardiol. 2011;50:433-41; Mazzanti A et al. J Am Coll Cardiol. 2014;63:1300-8; Giustetto C et al. HeartRhythm Case Rep. 2015;1:373-378; Harrell DT et al. Int. J Cardiol. 2015;190:393-402; Hu D et al. JACC Clinical Electrophysiology. 2017;3(7)727-743). In addition, in vitro functional studies have reported this alteration to result in altered channel function, suggesting a gain of function effect (Lees-Miller JP et al. Biophys J. 2009;96:3600-10; Sun Y et al. J Mol Cell Cardiol. 2011;50:433-41; El Harchi A et al. PLoS ONE. 2012;7:e52451; Hu D et al. JACC Clinical Electrophysiology. 2017;3(7)727-743). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Short 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 Short QT syndrome in the following publications (PMID:21130771). 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	1.0
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.97	.;D;D
Eigen	Uncertain	0.66
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Benign	0.68	T;T;T
M_CAP	Pathogenic	0.91	D
MetaRNN	Pathogenic	0.95	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	2.9	.;M;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-5.9	D;D;.
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D;D;.
Sift4G	Pathogenic	0.0010	D;D;D
Polyphen		0.76	P;D;.
Vest4		0.94
MutPred		0.70		.;Gain of sheet (P = 0.1208);.;
MVP		0.99
MPC		2.3
ClinPred		1.0	D
GERP RS		4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
Varity_R		0.92
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs199472947; hg19: chr7-150648628;