Hereditary neuropathy or pain disorder
Gene: SETXComment on phenotypes: SETX variants are also associated with Amyotrophic lateral sclerosis 4, juvenile, OMIM:602433, but this condition is not relevant to this narrow panel.Created: 19 Apr 2022, 2 p.m. | Last Modified: 19 Apr 2022, 2 p.m.
Panel Version: 1.100
Comment on 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 variantCreated: 19 Apr 2022, 1:57 p.m. | Last Modified: 19 Apr 2022, 1:57 p.m.
Panel Version: 1.99
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Spinocerebellar ataxia, autosomal recessive 1, OMIM:606002
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 reviewCreated: 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.
Variants in this GENE are reported as part of current diagnostic practice
Variants in this GENE are reported as part of current diagnostic practice
Comment on list classification: Neuropathy a common feature in SCAR1Created: 8 Jul 2016, 4:09 a.m.
Comment on mode of inheritance: SCA is biallelicCreated: 8 Jul 2016, 4:08 a.m.
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.
Three families originally described (different mutations), identified by linkage and sanger seq of region. Knock in mouse with phenotypesCreated: 9 Dec 2015, 8:50 a.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Only single family describedCreated: 8 Dec 2015, 3:06 p.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes for gene: SETX were changed from to Spinocerebellar ataxia, autosomal recessive 1, OMIM:606002
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
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