Long QT syndrome

Gene: SNTA1

Red List (low evidence)

SNTA1 (syntrophin alpha 1)
EnsemblGeneIds (GRCh38): ENSG00000101400
EnsemblGeneIds (GRCh37): ENSG00000101400
OMIM: 601017, Gene2Phenotype
SNTA1 is in 2 panels

9 reviews

Rebecca Whittington (South West GLH)

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

Matthew Edwards (Clinical Genetics & Genomics Lab, Royal Brompton & Harefield NHS Trust)

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

James Eden (Manchester)

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

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

Eleanor Williams (Genomics England Curator)

Comment on phenotypes: Added missing phenotype from OMIM
Created: 16 Jan 2019, 11:54 a.m.

Bill Newman (Manchester Centre for Genomic Medicine)

Green List (high evidence)

Caroline Wright (Genomics England Curator)

Comment on list classification: On Manchester diagnostic panel
Created: 7 Mar 2016, 4:25 p.m.

Ellen McDonagh (Genomics England Curator)

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.

Damian Smedley (Genomics England Curator)

Comment when marking as ready: Evidence from OMIM as well
Created: 1 Feb 2016, 9:04 p.m.

Oxford Medical Genetics Laboratory (OUH NHS Foundation Trust)

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • UKGTN
  • Expert list
  • Emory Genetics Laboratory
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Long QT syndrome 12 612955
  • Long QT syndrome 12 (612955)
OMIM
601017
Clinvar variants
Variants in SNTA1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

4 Mar 2019, Gel status: 1

Entity classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

Gene: snta1 has been classified as Red List (Low Evidence).

4 Mar 2019, Gel status: 1

Entity classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

Gene: snta1 has been classified as Red List (Low Evidence).

21 Feb 2019, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

Source South West GLH was added to SNTA1.

20 Feb 2019, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

Source London South GLH was added to SNTA1.

14 Feb 2019, Gel status: 3

Added New Source, Set Phenotypes, Set publications, Status Update

Ellen McDonagh (Genomics England Curator)

Source North West GLH was added to SNTA1. Added phenotypes Long QT syndrome 12 (612955) for gene: SNTA1 Publications for gene SNTA1 were changed from to 19684871 Rating Changed from Green List (high evidence) to Green List (high evidence)

16 Jan 2019, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: SNTA1 were changed from to Long QT syndrome 12 612955

7 Mar 2016, Gel status: 4

Gene classified by Genomics England curator

Caroline Wright (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

4 Mar 2016, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

1 Feb 2016, Gel status: 4

Gene classified by Genomics England curator

Damian Smedley (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

1 Feb 2016, Gel status: 3

Set Mode of Inheritance

Damian Smedley (Genomics England Curator)

Mode of inheritance for SNTA1 was changed to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

13 Jul 2015, Gel status: 3

Added New Source

Ellen McDonagh (Genomics England Curator)

SNTA1 was added to Long QT syndromepanel. Sources: UKGTN

13 Jul 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SNTA1 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

13 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SNTA1 was added to Long QT syndromepanel. Sources: Illumina TruGenome Clinical Sequencing Services,Emory Genetics Laboratory,Expert list

13 Jul 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SNTA1 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

13 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SNTA1 was added to Long QT syndromepanel. Sources: Illumina TruGenome Clinical Sequencing Services,Emory Genetics Laboratory,Expert list

13 Jul 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SNTA1 was added to Long QT syndromepanel. Sources: Illumina TruGenome Clinical Sequencing Services,Emory Genetics Laboratory,Expert list