NM_000238.4(KCNH2):c.2689A>G (p.Lys897Glu) AND Cardiac arrhythmia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003592255.1

Allele description [Variation Report for NM_000238.4(KCNH2):c.2689A>G (p.Lys897Glu)]

NM_000238.4(KCNH2):c.2689A>G (p.Lys897Glu)

Gene:

KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q36.1

Genomic location:

Preferred name:

NM_000238.4(KCNH2):c.2689A>G (p.Lys897Glu)

HGVS:

NC_000007.14:g.150948447T>C
NG_008916.1:g.34480A>G
NM_000238.4:c.2689A>GMANE SELECT
NM_001406753.1:c.2401A>G
NM_172057.3:c.1669A>G
NP_000229.1:p.Lys897Glu
NP_000229.1:p.Lys897Glu
NP_001393682.1:p.Lys801Glu
NP_742054.1:p.Lys557Glu
NP_742054.1:p.Lys557Glu
LRG_288t1:c.2689A>G
LRG_288t3:c.1669A>G
LRG_288:g.34480A>G
LRG_288p1:p.Lys897Glu
LRG_288p3:p.Lys557Glu
NC_000007.13:g.150645535T>C
NM_000238.3:c.2689A>G
NM_172057.2:c.1669A>G
NR_176254.1:n.3097A>G
NR_176255.1:n.1970A>G

Protein change:

K557E

Molecular consequence:

NM_000238.4:c.2689A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406753.1:c.2401A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_172057.3:c.1669A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_176254.1:n.3097A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176255.1:n.1970A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Cardiac arrhythmia
Synonyms:: Cardiac rhythm disease
Identifiers:: EFO: EFO_0004269; MONDO: MONDO:0007263; MedGen: C0003811; Human Phenotype Ontology: HP:0011675

Recent activity

Clear Turn Off Turn On

nucellin, partial [Hordeum euclaston]
nucellin, partial [Hordeum euclaston]
gi|213998812|gb|ACJ60773.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004358304	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 25, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31696929, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004358304

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 25, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Variant frequencies of KCNQ1, KCNH2, and SCN5A in a Chinese inherited arrhythmia cohort and other disease cohorts undergoing genetic testing.

Li X, Liu N, Bai R.

Ann Hum Genet. 2020 Mar;84(2):161-168. doi: 10.1111/ahg.12359. Epub 2019 Nov 7.

PubMed [citation]

PMID:: 31696929

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV004358304.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This missense variant replaces lysine with glutamic acid at codon 897 of the KCNH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual suspected of having epilepsy and in an individual who was not affected with inherited arrhythmia but suspected of other cardiovascular disease (PMID: 31696929). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

ClinVar

Relating variation to medicine