NM_000238.4(KCNH2):c.910_916+11del AND Long QT syndrome

Clinical significance:Likely pathogenic (Last evaluated: Jun 28, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000706331.1

Allele description [Variation Report for NM_000238.4(KCNH2):c.910_916+11del]

NM_000238.4(KCNH2):c.910_916+11del

Gene:
KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q36.1
Genomic location:
Preferred name:
NM_000238.4(KCNH2):c.910_916+11del
HGVS:
  • NC_000007.14:g.150958052_150958069del
  • NG_008916.1:g.24862_24879del
  • NM_000238.4:c.910_916+11delMANE SELECT
  • NM_172056.2:c.910_916+11del
  • LRG_288t2:c.910_916+11del
  • LRG_288:g.24862_24879del
  • NC_000007.13:g.150655140_150655157del
  • NM_000238.3:c.910_916+11delAGCACCGGTGAGGGCGCC
Links:
dbSNP: rs1563169296
NCBI 1000 Genomes Browser:
rs1563169296
Molecular consequence:
  • NM_000238.4:c.910_916+11del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_172056.2:c.910_916+11del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Long QT syndrome (LQTS)
Identifiers:
MONDO: MONDO:0002442; MeSH: D008133; MedGen: C0023976; OMIM: PS192500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000835374Invitaecriteria provided, single submitter
Likely pathogenic
(Jun 28, 2018)
germlineclinical testing

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

Summary from all submissions

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000835374.1

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

Description

This variant is a gross deletion of the genomic region encompassing part of exon 4 (c.910_916+11del) of the KCNH2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with KCNH2-related disease. Loss-of-function variants in KCNH2 are known to be pathogenic (PMID: 19862833). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Oct 7, 2021

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