Long QT syndrome

Gene: SNTA1

I don't know

Long QT syndrome 12 (OMIM 612955)

Created: 25 Mar 2019, 4:30 p.m.

Rare LQT susceptibility gene - see Ueda paper for ? functional evidence. PMID:19684871. PMID:18591664. 23376825

Created: 25 Mar 2019, 4:27 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Variants in this GENE are reported as part of current diagnostic practice

Red List (low evidence)

Gene currently on Royal Brompton panel, but literature evidence is low (eg: PMID 19684871) and variants reported in the literature are at too-high allele frequencies in gnomAD.

Created: 19 Mar 2019, 4:18 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Red List (low evidence)

Gene currently tested on Manchester cardiac gene panel. Only class 1-3 variants detected to date. 18 variants listed on HGMD (accessed 29/01/2019). ClinGen Knowledge Base: gene not curated (accessed 29/01/2019).

Created: 14 Feb 2019, 1:38 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Long QT syndrome 12 (612955)

Publications

• 19684871

Variants in this GENE are reported as part of current diagnostic practice

Comment on phenotypes: Added missing phenotype from OMIM

Created: 16 Jan 2019, 11:54 a.m.

Green List (high evidence)

Comment on list classification: On Manchester diagnostic panel

Created: 7 Mar 2016, 4:25 p.m.

I don't know

Comment on list classification: This gene-disease was discussed in the NHSE GMS Cardiology Specialist Group meeting call on 25th January 2019, and it was confirmed that this should be demoted from Green to Red due to lack of evidence for Long QT syndrome.

Created: 4 Mar 2019, 9:07 p.m.

This gene was part of an initial gene list collated by Matthew Edwards Royal Brompton Hospital sent 16th Jan 2019 on behalf of the London South GLH for review by the GMS Cardiology Specialist Group. Only gene symbol from the Royal Brompton gene panel was provided - suggested initial gene rating and evidence for inclusion not provided with the list.

Created: 20 Feb 2019, 2:17 p.m.

On the Inherited Cardiac Condition Genes panel for Long QT syndrome reported in: Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes, Pua et al, Journal of Cardiovascular Translational Research, online Feb 2016 (doi:10.​1007/​s12265-016-9673-5). The panel contains disease-causing, putatively pathogenic, research and phenocopy genes, and it is unclear from the publication whether this gene falls into the disease-causing category. No. of mutations indicated in supplemental table = 3.

Created: 19 Feb 2016, 11:06 a.m.

Comment when marking as ready: Evidence from OMIM as well

Created: 1 Feb 2016, 9:04 p.m.

Red List (low evidence)

2 variants reported in the literature one of which Oxford lab classify as unlikely to be pathogenic (0.6% of Europeans on GnomAD). Limited functional evidence of link to arrhythmia - thought to act through interractions with SCN5A. Insufficient evidence to be green gene.

Created: 25 Jan 2019, 12:41 p.m.

Only a small number of case reports with segregation and functional evidence.

Created: 3 Mar 2016, 9:39 a.m.

Variants in this GENE are reported as part of current diagnostic practice