chr7-150951505-C-T

Position:

chr7-150951505-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 6P and 4B. PM1PM5PP3PP5BS2

The NM_000238.4(KCNH2):c.1888G>A(p.Val630Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,614,106 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V630A) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 34)

Exomes 𝑓: 0.0000089 ( 0 hom. )

Consequence

KCNH2
NM_000238.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3U:3

Conservation

PhyloP100: 6.02

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 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

PM5

Other missense variant is known to change same aminoacid residue: Variant chr7-150951504-A-G is described in Lovd as [Pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.745

PP5

Variant 7-150951505-C-T is Pathogenic according to our data. Variant chr7-150951505-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 222669.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=3, Likely_pathogenic=3}.

BS2

High AC in GnomAdExome4 at 13 AD,Digenic gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNH2	NM_000238.4 link	c.1888G>A	p.Val630Ile	missense_variant	7/15	ENST00000262186.10	NP_000229.1	Q12809-1Q15BH2A0A090N8Q0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNH2	ENST00000262186.10 link	c.1888G>A	p.Val630Ile	missense_variant	7/15	1	NM_000238.4	ENSP00000262186.5		Q12809-1

Frequencies

GnomAD3 genomes

AF:

0.0000263

AC:

AN:

152234

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:

0.000192

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000199

AC:

AN:

251466

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135914

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:

0.0000352

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.00000889

AC:

AN:

1461872

Hom.:

Cov.:

AF XY:

0.00000963

AC XY:

AN XY:

727242

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:

0.0000116

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.00000809

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

AF:

0.0000263

AC:

AN:

152234

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000192

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000441

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000329

Hom.:

Bravo

AF:

0.0000189

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.0000330

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3Uncertain:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Long QT syndrome

Pathogenic:1Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 08, 2024	This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 630 of the KCNH2 protein (p.Val630Ile). This variant is present in population databases (rs199472958, gnomAD 0.005%). This missense change has been observed in individual(s) with clinical features of KCNH2-related conditions (PMID: 28449774, 34363016). ClinVar contains an entry for this variant (Variation ID: 222669). 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 does not substantially affect KCNH2 function (PMID: 8799887). This variant disrupts the p.Val630 amino acid residue in KCNH2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9693036, 16432067, 23303164). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Aug 13, 2024	This missense variant replaces valine with isoleucine at codon 630 of the KCNH2 protein. This variant is found within a highly conserved pore region (a.a.612-632). Rare nontruncating variants in this region have been shown to be significantly overrepresented in individuals with long QT syndrome (PMID: 32893267). A functional study has shown that this variant has no significant impact on channel function (PMID: 8799887). This variant has been reported in five unrelated individuals affected with or suspected of having long QT syndrome (PMID: 30041777, 32893267, communication with external laboratories ClinVar SCV000263978.2, SCV002723839.1), and in an individual affected with Brugada syndrome (PMID: 34363016), ventricular arrhythmias (ClinVar SCV001754799.1), or sudden arrhythmic death syndrome (PMID: 28449774). This variant has also been observed in individuals with other conditions, including epilepsy, dilated cardiomyopathy and muscular dystrophy, and multiple congenital abnormalities (communication with external laboratories ClinVar SCV002723839.1, SCV001400343.4). This variant has been identified in 7/282860 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different missense variant occurring at the same codon, p.Val630Ala, has been determined to be pathogenic (ClinVar variation ID: 67319, Color), indicating that valine at this position is important for KCNH2 protein function. Although there is a suspicion for a pathogenic role, the available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 25, 2018	Variant summary: KCNH2 c.1888G>A (p.Val630Ile) results in a conservative amino acid change located in the Ion transport domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.5e-05 in 277200 control chromosomes (gnomAD). The variant, c.1888G>A, has been reported in the literature in individuals affected with sudden arrhythmic death syndrome and long QT syndrome (Lahrouchi_2017, Owen_2018). These data indicate that the variant may be associated with disease. In addition, other missense changes affecting the same codon, p.V630A and p.V630L, and nearby p.N629S, p.N629K, p.N629I, p.N629D, and p.S631A, have been reported in affected individuals suggesting this region could be important for KCNH2 protein function. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cite the variant as likely pathogenic. Therefore, based on the variant fulfilling the following ACMG criterias: PM1,PM5,PP3, and PP5, the variant was classified as likely pathogenic. -

Long QT syndrome 2

Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Sep 23, 2020	This c.1888G>A (p.Val630Ile) variant in the KCNH2 gene has been reported in two unrelated individuals affected with ventricular arrhythmias and sudden cardiac death (PMID: 30041777, 28449774). It is seen at low frequency (7/282860 alleles) in the gnomAD population database and is predicted to be deleterious by multiple in silico algorithms. Other variants affecting the same codon (p.Val630Ala and p.Val630Leu) have been determined to be likely pathogenic (PMID: 9693036, 16432067, 23303164, 9024139, 11854117, 15840476, 8799887). This variant was identified in an individual with a history of ventricular arrhythmias and syncope s/p ICD placement. Therefore, the c.1888G>A (p.Val630Ile) variant in the KCNH2 gene is classified as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Mar 23, 2015	- -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 14, 2024

The p.V630I variant (also known as c.1888G>A), located in coding exon 7 of the KCNH2 gene, results from a G to A substitution at nucleotide position 1888. The valine at codon 630 is replaced by isoleucine, an amino acid with highly similar properties. This variant has been detected in individuals with sudden death or features consistent with long QT syndrome (LQTS); however, in several cases, clinical details were limited or a second variant in a LQTS-related gene was also detected (Lahrouchi N et al. J. Am. Coll. Cardiol., 2017 May;69:2134-2145; Owen HJ et al. Int. J. Cardiol., 2018 Oct;268:132-136; Walsh R et al. Genet Med, 2021 Jan;23:47-58; Nafissi NA et al. Circ Genom Precis Med, 2022 Oct;15:e003675; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Pathogenic

0.19

BayesDel_noAF

Pathogenic

0.17

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.74

.;D;D

Eigen

Uncertain

0.28

Eigen_PC

Uncertain

0.25

FATHMM_MKL

Benign

0.75

LIST_S2

Uncertain

0.93

D;D;D

M_CAP

Pathogenic

0.67

MetaRNN

Pathogenic

0.74

D;D;D

MetaSVM

Pathogenic

0.92

MutationAssessor

Benign

1.6

.;L;.

PrimateAI

Pathogenic

0.81

PROVEAN

Benign

-0.97

N;N;.

REVEL

Pathogenic

0.73

Sift

Benign

0.14

T;D;.

Sift4G

Benign

0.10

T;D;T

Polyphen

0.85

P;P;.

Vest4

0.67

MVP

0.86

MPC

1.9

ClinPred

0.83

GERP RS

3.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.22

gMVP

0.90

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