Genes in panel

Hereditary neuropathy

Gene: SETX

Green List (high evidence)

SETX (senataxin)
EnsemblGeneIds (GRCh38): ENSG00000107290
EnsemblGeneIds (GRCh37): ENSG00000107290
OMIM: 608465, Gene2Phenotype
SETX is in 14 panels

7 reviews

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

The Neurology Specialist Test Group agreed that this gene was recommended for the WGS panel based on a broader phenotype view to include conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation eg. HSP. This panel includes conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation. This panel as going to be used for R78, but subsequently during the follow up call on 21st June with the Test Group it was agreed that it was more clinically relevant for R78 to be restricted to genes that are associated with isolated neuropathy and as a result a new panel was created https://panelapp.genomicsengland.co.uk/panels/846/ for this purpose.
Created: 7 Dec 2019, 6:08 p.m. | Last Modified: 7 Dec 2019, 6:08 p.m.
Panel Version: 1.352
Rating and review submitted on behalf of James Polke (Neurogenetics Laboratory,Institute of Neurology, London), on behalf of London North GLH for GMS Neurology specialist test group.
Created: 9 May 2019, 5 p.m.

James Polke (Neurogenetics Laboratory, Institute of Neurology, London)

Red List (low evidence)

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

Rita Horvath (Institute of Genetic Medicine, Newcastle University)

Green List (high evidence)

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

Richard Scott (Genomics England Curator)

Comment on list classification: Neuropathy a common feature in SCAR1
Created: 8 Jul 2016, 4:09 a.m.
Comment on mode of inheritance: SCA is biallelic
Created: 8 Jul 2016, 4:08 a.m.

Ellen McDonagh (Genomics England Curator)

Comment on list classification: This gene is in the Charcot Marie Tooth Disease section in the UCLH National Hospital for Neurology and Neurosurgery & Institute of Neurology (NHNN) Neurogenetics genetic testing manual, for testing of dHMN.
Created: 10 Jun 2016, 1:26 p.m.
Comment on list classification: Multiple variants and cases reported for spinocerebellar ataxia on OMIM.
Created: 5 May 2016, 9:43 a.m.

Alexander Rossor (UCL Institute of Neurology)

Green List (high evidence)

Three families originally described (different mutations), identified by linkage and sanger seq of region. Knock in mouse with phenotypes
Created: 9 Dec 2015, 8:50 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Mary Reilly (Institute of Neurology)

Green List (high evidence)

Only single family described
Created: 8 Dec 2015, 3:06 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • London North GLH
  • Expert Review Green
  • Expert list
OMIM
608465
Clinvar variants
Variants in SETX
Penetrance
Complete
Publications
  • PMID:25802885 - Identifiy one previously reported variant and three novel variants in 4 families. Report the variants found in CMT patients are likely nonpathogenic due to bioinformatics analysis. Report SETX c.7640T>C is a nonpathogenic rare variant
  • PMID: 25025039 - a likely pathogenic variant in SETX reported in a sporadic case with CMT2 and spasticity. Found with a REEP1 variant, and the authors assume digenic pathogenicity.
Panels with this gene

History Filter Activity

29 Apr 2019, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SETX.

29 Apr 2019, Gel status: 3

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SETX. Rating Changed from Green List (high evidence) to Green List (high evidence)

8 Jul 2016, Gel status: 4

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

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

8 Jul 2016, Gel status: 4

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

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

8 Jul 2016, Gel status: 2

Set Mode of Inheritance

Richard Scott (Genomics England Curator)

Mode of inheritance for SETX was changed to BIALLELIC, autosomal or pseudoautosomal

10 Jun 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).

5 May 2016, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for SETX were set to PMID:25802885 - Identifiy one previously reported variant and three novel variants in 4 families. Report the variants found in CMT patients are likely nonpathogenic due to bioinformatics analysis. Report SETX c.7640T>C is a nonpathogenic rare variant; PMID: 25025039 - a likely pathogenic variant in SETX reported in a sporadic case with CMT2 and spasticity. Found with a REEP1 variant, and the authors assume digenic pathogenicity.

5 May 2016, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for SETX were set to PMID:25802885 - report SETX c.7640T>C is a nonpathogenic rare variant; PMID: 25025039 - a likely pathogenic variant in SETX reported in a sporadic case with CMT2 and spasticity. Found with a REEP1 variant, and the authors assume digenic pathogenicity.

5 May 2016, Gel status: 1

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

20 Jul 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

SETX was added to Charcot-Marie-Tooth diseasepanel. Sources: Expert list