NC_000007.13:g.(?_150324807)_(150706375_?)del AND Long QT syndrome

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 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:: RCV004583455.1

Allele description

NC_000007.13:g.(?_150324807)_(150706375_?)del

Genes:

GIMAP1:GTPase, IMAP family member 1 [Gene - OMIM - HGNC]
GIMAP2:GTPase, IMAP family member 2 [Gene - OMIM - HGNC]
GIMAP5:GTPase, IMAP family member 5 [Gene - OMIM - HGNC]
GIMAP6:GTPase, IMAP family member 6 [Gene - OMIM - HGNC]
AOC1:amine oxidase copper containing 1 [Gene - OMIM - HGNC]
NOS3:nitric oxide synthase 3 [Gene - OMIM - HGNC]
KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
TMEM176A:transmembrane protein 176A [Gene - OMIM - HGNC]
TMEM176B:transmembrane protein 176B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q36.1

Genomic location:

Chr7: 150324807 - 150706375 (on Assembly GRCh37)

Preferred name:

NC_000007.13:g.(?_150324807)_(150706375_?)del

HGVS:

NC_000007.13:g.(?_150324807)_(150706375_?)del

Condition(s)

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

Recent activity

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neutrophil cytosol factor 1 isoform b [Mus musculus]
neutrophil cytosol factor 1 isoform b [Mus musculus]
gi|170172553|ref|NP_035006.3|

Protein
LOC130067970 [Homo sapiens]
LOC130067970 [Homo sapiens]
Gene ID:130067970

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064561	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 16, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10973849, 19862833, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064561

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 16, 2023)

unknown

clinical testing

PubMed (3)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Spectrum of mutations in long-QT syndrome genes. KVLQT1, HERG, SCN5A, KCNE1, and KCNE2.

Splawski I, Shen J, Timothy KW, Lehmann MH, Priori S, Robinson JL, Moss AJ, Schwartz PJ, Towbin JA, Vincent GM, Keating MT.

Circulation. 2000 Sep 5;102(10):1178-85.

PubMed [citation]

PMID:: 10973849

The genetic basis of long QT and short QT syndromes: a mutation update.

Hedley PL, Jørgensen P, Schlamowitz S, Wangari R, Moolman-Smook J, Brink PA, Kanters JK, Corfield VA, Christiansen M.

Hum Mutat. 2009 Nov;30(11):1486-511. doi: 10.1002/humu.21106. Review.

PubMed [citation]

PMID:: 19862833

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV005064561.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the KCNH2 gene has been identified. Loss-of-function variants in KCNH2 are known to be pathogenic (PMID: 10973849, 19862833). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with KCNH2-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jul 7, 2024

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