NM_000238.4(KCNH2):c.1129-18C>A AND Long QT syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 9, 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:: RCV003649110.1

Allele description

NM_000238.4(KCNH2):c.1129-18C>A

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.1129-18C>A

HGVS:

NC_000007.14:g.150952871G>T
NG_008916.1:g.30056C>A
NM_000238.4:c.1129-18C>AMANE SELECT
NM_001204798.2:c.109-18C>A
NM_001406753.1:c.841-18C>A
NM_001406755.1:c.952-18C>A
NM_001406756.1:c.841-18C>A
NM_001406757.1:c.829-18C>A
NM_172056.3:c.1129-18C>A
NM_172057.3:c.109-18C>A
LRG_288:g.30056C>A
NC_000007.13:g.150649959G>T

Molecular consequence:

NM_000238.4:c.1129-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001204798.2:c.109-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406753.1:c.841-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406755.1:c.952-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406756.1:c.841-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001406757.1:c.829-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_172056.3:c.1129-18C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_172057.3:c.109-18C>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

Recent activity

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cytoplasmic polyadenylation element-binding protein 2 isoform X5 [Homo sapiens]
cytoplasmic polyadenylation element-binding protein 2 isoform X5 [Homo sapiens]
gi|2462594916|ref|XP_054204904.1|

Protein
cytoplasmic polyadenylation element-binding protein 2 isoform X4 [Homo sapiens]
cytoplasmic polyadenylation element-binding protein 2 isoform X4 [Homo sapiens]
gi|2462594914|ref|XP_054204903.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004554074	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 9, 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

SCV004554074

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 9, 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 Invitae, SCV004554074.1

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

Description

This sequence change falls in intron 5 of the KCNH2 gene. It does not directly change the encoded amino acid sequence of the KCNH2 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCNH2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

#	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: Feb 28, 2024

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