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NM_000238.4(KCNH2):c.2696C>T (p.Thr899Met) AND Cardiovascular phenotype

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 20, 2021
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:
RCV002429733.9

Allele description [Variation Report for NM_000238.4(KCNH2):c.2696C>T (p.Thr899Met)]

NM_000238.4(KCNH2):c.2696C>T (p.Thr899Met)

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.2696C>T (p.Thr899Met)
HGVS:
  • NC_000007.14:g.150947875G>A
  • NG_008916.1:g.35052C>T
  • NM_000238.2:c.2696C>T
  • NM_000238.4:c.2696C>TMANE SELECT
  • NM_172057.3:c.1676C>T
  • NP_000229.1:p.Thr899Met
  • NP_742054.1:p.Thr559Met
  • LRG_288t1:c.2696C>T
  • LRG_288t3:c.1676C>T
  • LRG_288:g.35052C>T
  • NC_000007.13:g.150644963G>A
  • NM_000238.3:c.2696C>T
  • NM_000238.4:c.2696C>T
  • NM_172057.2:c.1676C>T
Protein change:
T559M
Links:
dbSNP: rs1480554629
NCBI 1000 Genomes Browser:
rs1480554629
Molecular consequence:
  • NM_000238.4:c.2696C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172057.3:c.1676C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002742699Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 20, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Ambry Genetics, SCV002742699.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The p.T899M variant (also known as c.2696C>T), located in coding exon 12 of the KCNH2 gene, results from a C to T substitution at nucleotide position 2696. The threonine at codon 899 is replaced by methionine, an amino acid with similar properties. This alteration has been reported in a long QT syndrome and Brugada syndrome cohort (Li X et al. Ann Hum Genet, 2020 03;84:161-168). This amino acid position is poorly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024