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NM_000238.4(KCNH2):c.1039C>T (p.Pro347Ser) AND Long QT syndrome

Germline classification:
Benign/Likely benign (3 submissions)
Last evaluated:
Jan 31, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000148527.24

Allele description [Variation Report for NM_000238.4(KCNH2):c.1039C>T (p.Pro347Ser)]

NM_000238.4(KCNH2):c.1039C>T (p.Pro347Ser)

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.1039C>T (p.Pro347Ser)
Other names:
p.P347S:CCC>TCC
HGVS:
  • NC_000007.14:g.150957380G>A
  • NG_008916.1:g.25547C>T
  • NM_000238.4:c.1039C>TMANE SELECT
  • NM_001406753.1:c.751C>T
  • NM_001406755.1:c.862C>T
  • NM_001406756.1:c.751C>T
  • NM_001406757.1:c.739C>T
  • NM_172056.3:c.1039C>T
  • NP_000229.1:p.Pro347Ser
  • NP_000229.1:p.Pro347Ser
  • NP_001393682.1:p.Pro251Ser
  • NP_001393684.1:p.Pro288Ser
  • NP_001393685.1:p.Pro251Ser
  • NP_001393686.1:p.Pro247Ser
  • NP_742053.1:p.Pro347Ser
  • NP_742053.1:p.Pro347Ser
  • LRG_288t1:c.1039C>T
  • LRG_288t2:c.1039C>T
  • LRG_288:g.25547C>T
  • LRG_288p1:p.Pro347Ser
  • LRG_288p2:p.Pro347Ser
  • NC_000007.13:g.150654468G>A
  • NM_000238.2:c.1039C>T
  • NM_000238.3:c.1039C>T
  • NM_172056.2:c.1039C>T
  • NR_176254.1:n.1447C>T
  • Q12809:p.Pro347Ser
Protein change:
P247S
Links:
UniProtKB: Q12809#VAR_009912; dbSNP: rs138776684
NCBI 1000 Genomes Browser:
rs138776684
Molecular consequence:
  • NM_000238.4:c.1039C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406753.1:c.751C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406755.1:c.862C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406756.1:c.751C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406757.1:c.739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172056.3:c.1039C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Long QT syndrome (LQTS)
Identifiers:
MONDO: MONDO:0002442; MeSH: D008133; MedGen: C0023976

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000055217Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq
criteria provided, single submitter

(Ng et al. (Circ Cardiovasc Genet. 2013))
Likely benign
(Jun 24, 2013)
unknownresearch

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

SCV000190239CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation
no assertion criteria provided
Uncertain significance
(Jun 1, 2014)
germlineresearch

SCV000283956Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 31, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknown1not providednot providednot providednot providedresearch
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research

Citations

PubMed

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]
PMID:
23861362
PMCID:
PMC3887521

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000055217.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot provided1not providednot providednot provided

From CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190239.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000283956.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024