NM_000238.4(KCNH2):c.2653C>T (p.Arg885Cys) AND Cardiovascular phenotype

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 27, 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:: RCV002453373.9

Allele description [Variation Report for NM_000238.4(KCNH2):c.2653C>T (p.Arg885Cys)]

NM_000238.4(KCNH2):c.2653C>T (p.Arg885Cys)

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.2653C>T (p.Arg885Cys)

HGVS:

NC_000007.14:g.150948483G>A
NG_008916.1:g.34444C>T
NM_000238.4:c.2653C>TMANE SELECT
NM_172057.3:c.1633C>T
NP_000229.1:p.Arg885Cys
NP_000229.1:p.Arg885Cys
NP_742054.1:p.Arg545Cys
LRG_288t1:c.2653C>T
LRG_288:g.34444C>T
LRG_288p1:p.Arg885Cys
NC_000007.13:g.150645571G>A
NM_000238.3:c.2653C>T
Q12809:p.Arg885Cys

Protein change:

R545C

Links:

UniProtKB: Q12809#VAR_074886; dbSNP: rs143512106

NCBI 1000 Genomes Browser:

rs143512106

Molecular consequence:

NM_000238.4:c.2653C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172057.3:c.1633C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

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LOW QUALITY PROTEIN: E3 SUMO-protein ligase KIAA1586-like [Pantherophis guttatus...
LOW QUALITY PROTEIN: E3 SUMO-protein ligase KIAA1586-like [Pantherophis guttatus]
gi|2616717298|ref|XP_060547142.1|

Protein
putative protocadherin beta-18 [Pantherophis guttatus]
putative protocadherin beta-18 [Pantherophis guttatus]
gi|2616717279|ref|XP_060547135.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002739440	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Sep 27, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 17210839, 18222468, 18752142, 19716085, 27920829, 30369311 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002739440

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Sep 27, 2022)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

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

Prevalence of long-QT syndrome gene variants in sudden infant death syndrome.

Arnestad M, Crotti L, Rognum TO, Insolia R, Pedrazzini M, Ferrandi C, Vege A, Wang DW, Rhodes TE, George AL Jr, Schwartz PJ.

Circulation. 2007 Jan 23;115(3):361-7. Epub 2007 Jan 8.

PubMed [citation]

PMID:: 17210839

Cardiac potassium channel dysfunction in sudden infant death syndrome.

Rhodes TE, Abraham RL, Welch RC, Vanoye CG, Crotti L, Arnestad M, Insolia R, Pedrazzini M, Ferrandi C, Vege A, Rognum T, Roden DM, Schwartz PJ, George AL Jr.

J Mol Cell Cardiol. 2008 Mar;44(3):571-81. doi: 10.1016/j.yjmcc.2007.11.015. Epub 2007 Dec 7.

PubMed [citation]

PMID:: 18222468
PMCID:: PMC2386856

See all PubMed Citations (6)

Details of each submission

From Ambry Genetics, SCV002739440.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

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.

#	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: Nov 3, 2024

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