Undiagnosed metabolic disorders
Gene: SETXEnsemblGeneIds (GRCh38): ENSG00000107290
EnsemblGeneIds (GRCh37): ENSG00000107290
OMIM: 608465, Gene2Phenotype
SETX is in 13 panels
2 reviews
Catherine Snow (Genomics England)
Promoted from Amber to Green. SETX is associated with two phenotypes on OMIM. There are >3 unrelated cases listed on OMIM for both these phenotypes. Therefore, enough evidence for this gene to be promoted to Green status.Created: 5 Nov 2019, 11:14 a.m. | Last Modified: 5 Nov 2019, 11:14 a.m.
Panel Version: 1.410
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Amyotrophic lateral sclerosis 4, juvenile, 602433; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2, 606002
Sarah Leigh (Genomics England Curator)
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:02 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:02 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:02 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:01 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:01 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)Created: 6 Jan 2017, 2:01 p.m.
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Spinocerebellar ataxia, autosomal recessive 1, OMIM:606002; Amyotrophic lateral sclerosis 4, juvenile, OMIM:602433
Details
- Mode of Inheritance
- BOTH monoallelic and biallelic, autosomal or pseudoautosomal
- Sources
-
- Expert Review Green
- Literature
- Phenotypes
-
- Spinocerebellar ataxia, autosomal recessive 1, OMIM:606002
- Amyotrophic lateral sclerosis 4, juvenile, OMIM:602433
- OMIM
- 608465
- Clinvar variants
- Variants in SETX
- Penetrance
- Complete
- Publications
- Panels with this gene
-
- Hereditary ataxia
- Hereditary neuropathy or pain disorder
- Amyotrophic lateral sclerosis/motor neuron disease
- Undiagnosed metabolic disorders
- Adult onset neurodegenerative disorder
- Intellectual disability
- Childhood onset dystonia, chorea or related movement disorder
- Likely inborn error of metabolism
- Hereditary ataxia with onset in adulthood
- Hereditary neuropathy
- Paediatric motor neuronopathies
- Ataxia and cerebellar anomalies - narrow panel
- Albinism or congenital nystagmus
History Filter Activity
Set Phenotypes
Sarah Leigh (Genomics England Curator)Phenotypes for gene: SETX were changed from Secondary CoQ10 deficiency (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Amyotrophic lateral sclerosis/motor neuron disease; Charcot-Marie-Tooth disease; Hereditary ataxia to Spinocerebellar ataxia, autosomal recessive 1, OMIM:606002; Amyotrophic lateral sclerosis 4, juvenile, OMIM:602433
Entity classified by Genomics England curator
Catherine Snow (Genomics England)Gene: setx has been classified as Green List (High Evidence).
panel promoted to version 1
Sarah Leigh (Genomics England Curator)Construction of “Undiagnosed Metabolic Disorders” (UDM) panel • The 614 genes from the neurometabolic gene panel (PMID: 27604308) added • Green genes downloaded from V1 metabolic panels (Cerebral folate deficiency, Congenital disorders of glycosylation, Hyperammonaemia, Ketotic hypoglycaemia, Mitochondrial disorders, Mucopolysaccharideosis, Gaucher, Fabry, Peroxisomal disorders), sources replaced with "Expert review green", then loaded as a review onto UDM panel, resulting in 367 green genes and 333 red (therefore 86 new green genes included from the additional metabolic panels that weren't previously on the UDM panel) • Downloaded green genes from all panels. Removed genes from none V1 panels. Removed genes from the metabolic panels mentioned above. Compared the remaining genes with the red genes from UDM panel. Loaded as an "Expert review Amber" review to the overlapping genes, (the panel name where the genes came from was used as the phenotype) • Used variant information from PMID 27604308 to review the genes on this panel • Reviewed genes on UDM panel with genes from Emory "Inherited Metabolic Disorders: Sequencing Panel" and UKGTN “Inborn Errors of Metabolism 226 panel”, changing status where appropriate, added 14 UKGTN genes that had not be listed before • Review 10 red genes that had not previously been reviewed, 4/10 were reclassified as green • Review the remaining 145 red genes that had not previously been reviewed (shared between reviewers EM, RF, LD, AT, HB, ON & SL), resulting in 60 green, 11 amber, 70 red, 4 I don’t know reviews) • Reviewed genes from PMID: 24816252 as a publication to genes found in the Inborn error or metabolism Genes metabolomics GWAS paper (figure 5). 2 new genes added
Set Mode of Inheritance
Sarah Leigh (Genomics England Curator)Mode of inheritance for SETX was changed to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Set Mode of Inheritance
Sarah Leigh (Genomics England Curator)Model of inheritance for gene SETX was set to BIALLELIC, autosomal or pseudoautosomal
Set Mode of Inheritance, Added New Source
Sarah Leigh (Genomics England Curator)SETX was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Amber Model of inheritance for gene SETX was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Added New Source
Sarah Leigh (Genomics England Curator)SETX was added to Undiagnosed metabolic disorderspanel. Sources: Literature
Created
Sarah Leigh (Genomics England Curator)SETX was created by sleigh