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NM_000238.4(KCNH2):c.2690A>T (p.Lys897Met) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 4, 2017
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:
RCV000181882.11

Allele description [Variation Report for NM_000238.4(KCNH2):c.2690A>T (p.Lys897Met)]

NM_000238.4(KCNH2):c.2690A>T (p.Lys897Met)

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.2690A>T (p.Lys897Met)
Other names:
p.K897M:AAG>ATG
HGVS:
  • NC_000007.14:g.150948446T>A
  • NG_008916.1:g.34481A>T
  • NM_000238.4:c.2690A>TMANE SELECT
  • NM_172057.3:c.1670A>T
  • NP_000229.1:p.Lys897Met
  • NP_000229.1:p.Lys897Met
  • NP_742054.1:p.Lys557Met
  • LRG_288t1:c.2690A>T
  • LRG_288:g.34481A>T
  • LRG_288p1:p.Lys897Met
  • NC_000007.13:g.150645534T>A
  • NM_000238.2:c.2690A>T
  • NM_000238.3:c.2690A>T
  • NM_172057.1:c.1670A>T
Protein change:
K557M
Links:
dbSNP: rs1805123
NCBI 1000 Genomes Browser:
rs1805123
Molecular consequence:
  • NM_000238.4:c.2690A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172057.3:c.1670A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000234185GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 4, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000234185.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

p.Lys897Met (AAG>ATG): c.2690 A>T in exon 11 of the KCNH2 (aka HERG) gene (NM_000238.2). The Lys897Met variant in the KCNH2 gene has not been reported as a disease-causing mutation or as a benign polymorphism to our knowledge. Lys897Met results in a non-conservative amino acid substitution of a positively charged Lysine with a non-polar Methionine at a position that is conserved across species. Mutations in nearby codons (Arg894Cys, Arg894Leu, Gly903Arg) have been reported in association with LQTS, supporting the functional importance of this region of the protein. Also, the NHLBI ESP Exome Variant Server reports Lys897Met was not observed in approximately 6,500 samples from individuals of European and African American backgrounds, indicating it is not a common benign variant in these populations. Nevertheless, another missense change at this codon (Lys897Thr) has been reported as a polymorphism. With the clinical and molecular information available at this time, we cannot definitively determine if Lys897Met is a disease-causing mutation or a rare benign variant. The variant is found in LQT panel(s).

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

Last Updated: Nov 3, 2024