NM_000238.4(KCNH2):c.2678_2683del (p.Arg893_Arg894del) AND Long QT syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 3, 2023
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:: RCV002639000.3

Allele description [Variation Report for NM_000238.4(KCNH2):c.2678_2683del (p.Arg893_Arg894del)]

NM_000238.4(KCNH2):c.2678_2683del (p.Arg893_Arg894del)

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.2678_2683del (p.Arg893_Arg894del)

HGVS:

NC_000007.14:g.150948457_150948462del
NG_008916.1:g.34469_34474del
NM_000238.4:c.2678_2683delMANE SELECT
NM_001406753.1:c.2386_2391delCGCAGG
NM_172057.3:c.1658_1663del
NP_000229.1:p.Arg893_Arg894del
NP_000229.1:p.Arg893_Arg894del
NP_001393682.1:p.Arg797_Arg798del
NP_742054.1:p.Arg553_Arg554del
NP_742054.1:p.Arg553_Arg554del
LRG_288t1:c.2674_2679del
LRG_288t3:c.1654_1659del
LRG_288:g.34469_34474del
LRG_288p1:p.Arg893_Arg894del
LRG_288p3:p.Arg553_Arg554del
NC_000007.13:g.150645541_150645546del
NC_000007.13:g.150645545_150645550del
NM_000238.3:c.2674_2679delCGCAGG
NM_172057.2:c.1654_1659delCGCAGG
NR_176254.1:n.3082_3087delCGCAGG
NR_176255.1:n.1955_1960delCGCAGG

Molecular consequence:

NM_000238.4:c.2678_2683del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_172057.3:c.1658_1663del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406753.1:c.2386_2391delCGCAGG - 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
SCV002978302	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 3, 2023)	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

SCV002978302

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 3, 2023)

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, SCV002978302.2

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

Description

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 has not been reported in the literature in individuals affected with KCNH2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.2678_2683del, results in the deletion of 2 amino acid(s) of the KCNH2 protein (p.Arg893_Arg894del), 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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