NM_000238.4(KCNH2):c.562_570del (p.Ala188_Ala190del) AND Long QT syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 20, 2022
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:: RCV002637622.3

Allele description [Variation Report for NM_000238.4(KCNH2):c.562_570del (p.Ala188_Ala190del)]

NM_000238.4(KCNH2):c.562_570del (p.Ala188_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.562_570del (p.Ala188_Ala190del)

HGVS:

NC_000007.14:g.150958406_150958414del
NG_008916.1:g.24514_24522del
NM_000238.4:c.562_570delMANE SELECT
NM_001406753.1:c.273_281delCGCGGGCGC
NM_001406755.1:c.384_392delCGCGGGCGC
NM_001406756.1:c.273_281delCGCGGGCGC
NM_001406757.1:c.261_269delCGCGGGCGC
NM_172056.3:c.561_569delCGCGGGCGC
NP_000229.1:p.Ala188_Ala190del
NP_000229.1:p.Ala188_Ala190del
NP_001393682.1:p.Ala92_Ala94del
NP_001393684.1:p.Ala129_Ala131del
NP_001393685.1:p.Ala92_Ala94del
NP_001393686.1:p.Ala88_Ala90del
NP_742053.1:p.Ala188_Ala190del
NP_742053.1:p.Ala188_Ala190del
LRG_288t1:c.561_569del
LRG_288t2:c.562_570del
LRG_288:g.24514_24522del
LRG_288p1:p.Ala188_Ala190del
LRG_288p2:p.Ala188_Ala190del
NC_000007.13:g.150655493_150655501del
NC_000007.13:g.150655494_150655502del
NM_000238.3:c.561_569delCGCGGGCGC
NM_172056.2:c.562_570del
NR_176254.1:n.969_977delCGCGGGCGC

Molecular consequence:

NM_000238.4:c.562_570del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406753.1:c.273_281delCGCGGGCGC - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406755.1:c.384_392delCGCGGGCGC - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406756.1:c.273_281delCGCGGGCGC - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001406757.1:c.261_269delCGCGGGCGC - inframe_indel - [Sequence Ontology: SO:0001820]
NM_172056.3:c.561_569delCGCGGGCGC - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003518185	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 20, 2022)	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

SCV003518185

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 20, 2022)

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, SCV003518185.2

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

Description

This variant has not been reported in the literature in individuals affected with KCNH2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant is present in population databases (no rsID available, gnomAD 0.009%). This variant, c.562_570del, results in the deletion of 3 amino acid(s) of the KCNH2 protein (p.Ala188_Ala190del), but otherwise preserves the integrity of the reading frame.

#	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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