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Hereditary neuropathy NOT PMP22 copy number

Gene: SETX

Green List (high evidence)

SETX (senataxin)
EnsemblGeneIds (GRCh38): ENSG00000107290
EnsemblGeneIds (GRCh37): ENSG00000107290
OMIM: 608465, Gene2Phenotype
SETX is in 15 panels

7 reviews

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rated Green : From feedback from Genomics England Clinical team (Anna de Burca and Meriel McEntagart). Re-evaluation of evidence - demotion / James Polke Red review but no comment?? Pretty rare for this to present as a dominant juvenile ALS phenotype but three different mutations reported. Probably reasonable to keep as green but presumably in ALS panel. SETX had been reviewed by James Polke as Red but he had not left a comment, since he was not on the call, agreed that this gene be left as Green unless James provides an explanation for his Red review
Created: 6 Dec 2019, 2:44 p.m. | Last Modified: 6 Dec 2019, 2:49 p.m.
Panel Version: 0.37
This gene has changed ratings because the panel for R78 was going to be a broad panel (to include conditions where neuropathy is part of a more complex phenotype or where there is overlap with another neurological presentation eg. HSP) 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, which this panel represents. For genes that represent the broader phenotype see https://panelapp.genomicsengland.co.uk/panels/85/.
Created: 6 Dec 2019, 1:23 p.m. | Last Modified: 6 Dec 2019, 1:23 p.m.
Panel Version: 0.19
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
  • Expert list
  • Expert Review Green
  • London North GLH
  • NHS GMS
  • NHS GMS
  • London North GLH
OMIM
608465
Clinvar variants
Variants in SETX
Penetrance
None
Publications
  • 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.
  • 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
Panels with this gene

History Filter Activity

5 Dec 2019, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

gene: SETX was added gene: SETX was added to Hereditary neuropathy NOT PMP22 copy number. Sources: NHS GMS,London North GLH,Expert Review Green,Expert list Mode of inheritance for gene: SETX was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SETX were set to 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.; 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