NM_000238.4(KCNH2):c.2145+1G>A AND Long QT syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 16, 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:: RCV000477020.7

Allele description [Variation Report for NM_000238.4(KCNH2):c.2145+1G>A]

NM_000238.4(KCNH2):c.2145+1G>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.2145+1G>A

HGVS:

NC_000007.14:g.150950920C>T
NG_008916.1:g.32007G>A
NM_000238.4:c.2145+1G>AMANE SELECT
NM_001204798.2:c.1125+1G>A
NM_001406753.1:c.1857+1G>A
NM_001406755.1:c.1968+1G>A
NM_001406756.1:c.1857+1G>A
NM_001406757.1:c.1845+1G>A
NM_172056.3:c.2145+1G>A
NM_172057.3:c.1125+1G>A
LRG_288t1:c.2145+1G>A
LRG_288:g.32007G>A
NC_000007.13:g.150648008C>T
NM_000238.2:c.2145+1G>A
NM_000238.3:c.2145+1G>A

Links:

dbSNP: rs886039385

NCBI 1000 Genomes Browser:

rs886039385

Molecular consequence:

NM_000238.4:c.2145+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001204798.2:c.1125+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406753.1:c.1857+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406755.1:c.1968+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406756.1:c.1857+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406757.1:c.1845+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_172056.3:c.2145+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_172057.3:c.1125+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000543421	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 16, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 32383558, 16199547, 10973849, 19862833, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000543421

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 16, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Reclassification of genetic variants in children with long QT syndrome.

Westphal DS, Burkard T, Moscu-Gregor A, Gebauer R, Hessling G, Wolf CM.

Mol Genet Genomic Med. 2020 Sep;8(9):e1300. doi: 10.1002/mgg3.1300. Epub 2020 May 8.

PubMed [citation]

PMID:: 32383558
PMCID:: PMC7506994

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000543421.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 265192). Disruption of this splice site has been observed in individual(s) with long QT syndrome (PMID: 32383558). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 8 of the KCNH2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in KCNH2 are known to be pathogenic (PMID: 10973849, 19862833).

#	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

ClinVar

Relating variation to medicine