NM_000238.4(KCNH2):c.555_569del (p.Gly186_Ala190del) AND Long QT syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 14, 2017
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:: RCV000552293.4

Allele description [Variation Report for NM_000238.4(KCNH2):c.555_569del (p.Gly186_Ala190del)]

NM_000238.4(KCNH2):c.555_569del (p.Gly186_Ala190del)

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.555_569del (p.Gly186_Ala190del)

HGVS:

NC_000007.14:g.150958411_150958425del
NG_008916.1:g.24507_24521del
NM_000238.4:c.555_569delMANE SELECT
NM_001406753.1:c.262_276delGGCGCGGGCGGCGCG
NM_001406755.1:c.373_387delGGCGCGGGCGGCGCG
NM_001406756.1:c.262_276delGGCGCGGGCGGCGCG
NM_001406757.1:c.250_264delGGCGCGGGCGGCGCG
NM_172056.3:c.550_564delGGCGCGGGCGGCGCG
NP_000229.1:p.Gly186_Ala190del
NP_000229.1:p.Gly186_Ala190del
NP_001393682.1:p.Gly90_Ala94del
NP_001393684.1:p.Gly127_Ala131del
NP_001393685.1:p.Gly90_Ala94del
NP_001393686.1:p.Gly86_Ala90del
NP_742053.1:p.Gly186_Ala190del
NP_742053.1:p.Gly186_Ala190del
LRG_288t1:c.550_564del
LRG_288t2:c.555_569del
LRG_288:g.24507_24521del
LRG_288p1:p.Gly186_Ala190del
LRG_288p2:p.Gly186_Ala190del
NC_000007.13:g.150655499_150655513del
NM_000238.3:c.550_564delGGCGCGGGCGGCGCG
NM_000238.3:c.555_569delGGGCGGCGCGGGCGC
NM_172056.2:c.555_569del
NR_176254.1:n.958_972delGGCGCGGGCGGCGCG

Links:

dbSNP: rs1554427907

NCBI 1000 Genomes Browser:

rs1554427907

Molecular consequence:

NM_000238.4:c.555_569del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406753.1:c.262_276delGGCGCGGGCGGCGCG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406755.1:c.373_387delGGCGCGGGCGGCGCG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406756.1:c.262_276delGGCGCGGGCGGCGCG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406757.1:c.250_264delGGCGCGGGCGGCGCG - inframe_indel - [Sequence Ontology: SO:0001820]
NM_172056.3:c.550_564delGGCGCGGGCGGCGCG - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

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

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LPA lipoprotein(a) [Homo sapiens]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000627493	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 14, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000627493

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 14, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000627493.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.555_569del, results in the deletion of 5 amino acids of the KCNH2 protein (p.Gly186_Ala190del), but otherwise preserves the integrity of the reading frame. 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 a KCNH2-related disease. In summary, this variant has uncertain impact on KCNH2 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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