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NM_000238.4(KCNH2):c.2331C>T (p.Thr777=) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Oct 31, 2016
Review status:
criteria provided, conflicting classifications
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:
RCV000589926.17

Allele description [Variation Report for NM_000238.4(KCNH2):c.2331C>T (p.Thr777=)]

NM_000238.4(KCNH2):c.2331C>T (p.Thr777=)

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.2331C>T (p.Thr777=)
HGVS:
  • NC_000007.14:g.150950235G>A
  • NG_008916.1:g.32692C>T
  • NM_000238.4:c.2331C>TMANE SELECT
  • NM_001204798.2:c.1311C>T
  • NM_001406753.1:c.2043C>T
  • NM_001406755.1:c.2154C>T
  • NM_001406756.1:c.2043C>T
  • NM_001406757.1:c.2031C>T
  • NM_172056.3:c.2331C>T
  • NM_172057.3:c.1311C>T
  • NP_000229.1:p.Thr777=
  • NP_000229.1:p.Thr777=
  • NP_001191727.1:p.Thr437=
  • NP_001393682.1:p.Thr681=
  • NP_001393684.1:p.Thr718=
  • NP_001393685.1:p.Thr681=
  • NP_001393686.1:p.Thr677=
  • NP_742053.1:p.Thr777=
  • NP_742053.1:p.Thr777=
  • NP_742054.1:p.Thr437=
  • NP_742054.1:p.Thr437=
  • LRG_288t1:c.2331C>T
  • LRG_288t2:c.2331C>T
  • LRG_288t3:c.1311C>T
  • LRG_288:g.32692C>T
  • LRG_288p1:p.Thr777=
  • LRG_288p2:p.Thr777=
  • LRG_288p3:p.Thr437=
  • NC_000007.13:g.150647323G>A
  • NM_000238.2:c.2331C>T
  • NM_000238.3:c.2331C>T
  • NM_172056.2:c.2331C>T
  • NM_172057.2:c.1311C>T
  • NR_176254.1:n.2739C>T
  • NR_176255.1:n.1612C>T
Links:
dbSNP: rs41307292
NCBI 1000 Genomes Browser:
rs41307292
Molecular consequence:
  • NR_176254.1:n.2739C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176255.1:n.1612C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000238.4:c.2331C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001204798.2:c.1311C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406753.1:c.2043C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406755.1:c.2154C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406756.1:c.2043C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001406757.1:c.2031C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_172056.3:c.2331C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_172057.3:c.1311C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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
SCV000696023Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Oct 31, 2016) 		germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000701670Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Oct 19, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic polymorphisms in KCNQ1, HERG, KCNE1 and KCNE2 genes in the Chinese, Malay and Indian populations of Singapore.

Koo SH, Ho WF, Lee EJ.

Br J Clin Pharmacol. 2006 Mar;61(3):301-8.

PubMed [citation]
PMID:
16487223
PMCID:
PMC1885019

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696023.1

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

Description

Variant summary: The c.2331T>C (p.Thr777=) in KCNH2 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect a normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in control population dataset of ExAC at a frequency of 0.0001 (13/120792 chrs tested), predominantly in individuals of East Asian descent (0.001; 9/8618 chrs tested). These frequencies exceed the estimated maximal expected allele frequency of a pathogenic variant in KCNH2 gene (0.0001). The variant has not, to our knowledge, been reported in affected individuals via publications but was reported as a polymorphism in healthy Chinese controls (Koo, 2006). A clinical diagnostic laboratory cites the variant as a "VOUS." Therefore, taking all available lines of evidence into consideration, the variant of interest has been classified as Benign.

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

From Eurofins Ntd Llc (ga), SCV000701670.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 26, 2024