rs45610936

Positions:

chr21-34370846-CCT-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2

The NM_172201.2(KCNE2):c.369_370del(p.Ter124IlefsTer15) variant causes a frameshift, stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000855 in 1,613,704 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P123P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000086 ( 0 hom. )

Consequence

KCNE2
NM_172201.2 frameshift, stop_lost

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:5B:1

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

KCNE2 (HGNC:6242): (potassium voltage-gated channel subfamily E regulatory subunit 2) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, isk-related subfamily. This member is a small integral membrane subunit that assembles with the KCNH2 gene product, a pore-forming protein, to alter its function. This gene is expressed in heart and muscle and the gene mutations are associated with cardiac arrhythmia. [provided by RefSeq, Jul 2008]

KCNE2 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM4

Stoplost variant in NM_172201.2 Downstream stopcodon found after 107 codons.

BS2

High AC in GnomAd4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
KCNE2	NM_172201.2 linkuse as main transcript	c.369_370del	p.Ter124IlefsTer15	frameshift_variant, stop_lost	2/2	ENST00000290310.4
LOC105372791	XR_937683.3 linkuse as main transcript	n.1006_1007del		non_coding_transcript_exon_variant	2/2
LOC105372791	XR_007067848.1 linkuse as main transcript	n.1041_1042del		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNE2	ENST00000290310.4 linkuse as main transcript	c.369_370del	p.Ter124IlefsTer15	frameshift_variant, stop_lost	2/2	1	NM_172201.2	P1
	ENST00000440403.2 linkuse as main transcript	n.441_442del		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes

AF:

0.0000789

AC:

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000327

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000797

AC:

AN:

251094

Hom.:

AF XY:

0.0000663

AC XY:

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.000124

Gnomad AMR exome

AF:

0.000202

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000881

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000862

AC:

126

AN:

1461534

Hom.:

AF XY:

0.0000811

AC XY:

AN XY:

727082

show subpopulations

Gnomad4 AFR exome

AF:

0.0000896

Gnomad4 AMR exome

AF:

0.000291

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000926

Gnomad4 OTH exome

AF:

0.0000663

GnomAD4 genome

AF:

0.0000789

AC:

AN:

152170

Hom.:

Cov.:

AF XY:

0.000108

AC XY:

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000214

Hom.:

Bravo

AF:

0.0000945

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:5Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Atrial fibrillation, familial, 4;C3150953:Long QT syndrome 6

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	New York Genome Center	Apr 20, 2022	The c.369_370delCT variant has previously been reported in an individual with sudden infant death syndrome [PMID: 29544605] and in a patient with LQT phenotype [PMID:19716085]. The variant was also observed in another patient with LQT phenotype as well as in three asymptomatic relatives with normal QT interval [PMID: 28794082]. This variant has been deposited in ClinVar [ClinVar ID: 190797] as a Variant of Uncertain Significance. The variant c.369_370delCT is observed in 51 alleles (~ 0.009% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.369_370delCT variant is located in the last exon of this 2-exon gene, replaces the canonical stop codon with Isoleucine residue and is predicted to extend the length of KCNE2 protein at the C-terminus by an additional 14 amino acids. Functional consequences of these predicted additional amino acids are unknown at this time. Based on available evidence, this c.369_370delCT p.(Ter124IleextTer?) variant identified in KCNE2 gene is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jul 23, 2021	- -

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Apr 22, 2022

Reported in association with LQTS, SCD, and SIDS (Kapplinger et al., 2009; Roberts et al., 2017; Tester et al., 2018); however, it was shown to segregate in three asymptomatic relatives with normal QTc intervals (Roberts et al., 2017); Normal stop codon changed to an isoleucine codon, leading to the addition of 14 amino acids at the C-terminus; This variant is associated with the following publications: (PMID: 29544605, 28794082, 19716085) -

KCNE2-related disorder

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Oct 26, 2018

The KCNE2 c.369_370delCT (p.Ter124Ile) variant is a stop-loss variant that is predicted to result in an elongation of the protein. The p.Ter124Ile variant has been reported in a single study and found in one individual referred for long QT syndrome genetic testing (Kapplinger et al. 2009). Four other genes, including the three major contributors to long QT syndrome, were also screened for variants in this patient. The variant was absent from over 1300 healthy control individuals and is reported at a frequency of 0.000203 in the Latino population of the Genome Aggregation Database. The p.Ter124Ile variant has not been reported in the literature in association with familial atrial fibrillation. Based on the evidence and the potential impact of stop-lost variants, the p.Ter124Ile variant is classified as a variant of unknown significance but suspicious for pathogenicity for KCNE2-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Long QT syndrome 6

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Nov 09, 2023

This sequence change disrupts the translational stop signal of the KCNE2 mRNA. It is expected to extend the length of the KCNE2 protein by 14 additional amino acid residues. This variant is present in population databases (rs45610936, gnomAD 0.02%). This protein extension has been observed in individual(s) with sudden unexplained death or clinical features of long QT syndrome (PMID: 19716085, 28794082, 29544605). This variant is also known as Pro123fsTer16. ClinVar contains an entry for this variant (Variation ID: 190797). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. -

Cardiovascular phenotype

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 07, 2022

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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