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NM_000238.4(KCNH2):c.3152+1G>T AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 11, 2016
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:
RCV000414266.1

Allele description [Variation Report for NM_000238.4(KCNH2):c.3152+1G>T]

NM_000238.4(KCNH2):c.3152+1G>T

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.3152+1G>T
HGVS:
  • NC_000007.14:g.150947327C>A
  • NG_008916.1:g.35600G>T
  • NM_000238.4:c.3152+1G>TMANE SELECT
  • NM_001406753.1:c.2864+1G>T
  • NM_172057.3:c.2132+1G>T
  • LRG_288:g.35600G>T
  • NC_000007.13:g.150644415C>A
  • NM_000238.2:c.3152+1G>T
Links:
dbSNP: rs1057518151
NCBI 1000 Genomes Browser:
rs1057518151
Molecular consequence:
  • NM_000238.4:c.3152+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406753.1:c.2864+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_172057.3:c.2132+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000491582GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Oct 11, 2016) 		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, SCV000491582.2

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

Description

Although the c.3152+1 G>T pathogenic variant in the KCNH2 gene has not been reported as a pathogenic variant or as a benign variant to our knowledge, it destroys the canonical splice donor site in intron 13 and is predicted to cause abnormal gene splicing. This variant is predicted to lead to either an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Other downstream splice site variants in the KCNH2 gene and a different pathogenic variant affecting the same nucleotide (c.3152+1 G>A) have been reported in HGMD in association with LQTS (Stenson et al., 2014). Furthermore, the c.3152+1 G>T variant was not observed in approximately 5,800 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project (average read depth 6X).In summary, c.3152+1 G>T in the KCNH2 gene is interpreted as a pathogenic variant.

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

Last Updated: Sep 29, 2024