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NM_000238.4(KCNH2):c.526C>T (p.Arg176Trp) AND Long QT syndrome

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 31, 2024
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:
RCV000199086.19

Allele description [Variation Report for NM_000238.4(KCNH2):c.526C>T (p.Arg176Trp)]

NM_000238.4(KCNH2):c.526C>T (p.Arg176Trp)

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.526C>T (p.Arg176Trp)
Other names:
p.R176W:CGG>TGG
HGVS:
  • NC_000007.14:g.150958449G>A
  • NG_008916.1:g.24478C>T
  • NM_000238.4:c.526C>TMANE SELECT
  • NM_001406753.1:c.238C>T
  • NM_001406755.1:c.349C>T
  • NM_001406756.1:c.238C>T
  • NM_001406757.1:c.226C>T
  • NM_172056.3:c.526C>T
  • NP_000229.1:p.Arg176Trp
  • NP_000229.1:p.Arg176Trp
  • NP_001393682.1:p.Arg80Trp
  • NP_001393684.1:p.Arg117Trp
  • NP_001393685.1:p.Arg80Trp
  • NP_001393686.1:p.Arg76Trp
  • NP_742053.1:p.Arg176Trp
  • NP_742053.1:p.Arg176Trp
  • LRG_288t1:c.526C>T
  • LRG_288t2:c.526C>T
  • LRG_288:g.24478C>T
  • LRG_288p1:p.Arg176Trp
  • LRG_288p2:p.Arg176Trp
  • NC_000007.13:g.150655537G>A
  • NM_000238.2:c.526C>T
  • NM_000238.3:c.526C>T
  • NM_172056.2:c.526C>T
  • NR_176254.1:n.934C>T
  • Q12809:p.Arg176Trp
Protein change:
R117W
Links:
UniProtKB: Q12809#VAR_008915; dbSNP: rs36210422
NCBI 1000 Genomes Browser:
rs36210422
Molecular consequence:
  • NM_000238.4:c.526C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406753.1:c.238C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406755.1:c.349C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406756.1:c.238C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406757.1:c.226C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172056.3:c.526C>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
SCV000253125Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

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

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

SCV000987628Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Nov 10, 2022)
germlineclinical testing

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

SCV004021959Dept of Medical Biology, Uskudar University
criteria provided, single submitter

(Dept of Medical Biology Variant Classification)
Uncertain significance
(Jan 8, 2024)
paternalresearch

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
Turkishpaternalyes1not providednot providednot providednot providedresearch

Citations

PubMed

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000253125.10

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

From Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute, SCV000987628.2

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

Description

Risk factor for disease development: PS4; PP1_strong; PS3_mod; PP2; PP3; BS1; BS2

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

From Dept of Medical Biology, Uskudar University, SCV004021959.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Turkish1not providednot providedresearchnot provided

Description

Criteria: BS1, PP2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024