Genes in panel
STRs in panel
Prev Next

Undiagnosed metabolic disorders

Gene: SPTLC1

Green List (high evidence)

SPTLC1 (serine palmitoyltransferase long chain base subunit 1)
EnsemblGeneIds (GRCh38): ENSG00000090054
EnsemblGeneIds (GRCh37): ENSG00000090054
OMIM: 605712, Gene2Phenotype
SPTLC1 is in 9 panels

2 reviews

Catherine Snow (Genomics England)

Green List (high evidence)

Promoted from Amber to Green. This gene is associated with a relevant disease in OMIM and there is enough evidence to support a gene-disease association.

SPTLC1, encodes one of the two subunits of serine palmitoyltransferase (SPT), the enzyme catalyzing the first and rate-limiting step in the de novo synthesis of sphingolipids. PMID 20097765 reports that mutations in SPTLC1 cause a gain of function mechanism, which results in the formation of two atypical and neurotoxic sphingolipid metabolites.

Confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/) and in sufficient publications.
Created: 26 Sep 2019, 9:56 a.m. | Last Modified: 26 Sep 2019, 9:56 a.m.
Panel Version: 1.314

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Neuropathy, hereditary sensory and autonomic, type IA, 162400

Publications

Mode of pathogenicity
Other

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, 2:03 p.m.
Amber review assigned as this gene is Green on the V1 panel(s) named as a phenotype(s)
Created: 6 Jan 2017, 2:03 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.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Familial dysautonomia

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Serine palmitoyl transferase deficiency (Disorders of complex lipid synthesis)
  • Charcot-Marie-Tooth disease
  • Familial dysautonomia
OMIM
605712
Clinvar variants
Variants in SPTLC1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

26 Sep 2019, Gel status: 3

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC1 were set to 27604308

26 Sep 2019, Gel status: 3

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: sptlc1 has been classified as Green List (High Evidence).

27 Feb 2017, Gel status: 2

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

6 Jan 2017, Gel status: 2

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for SPTLC1 was changed to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

6 Jan 2017, Gel status: 2

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

6 Jan 2017, Gel status: 2

Set Mode of Inheritance, Added New Source

Sarah Leigh (Genomics England Curator)

SPTLC1 was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Amber Model of inheritance for gene SPTLC1 was set to BIALLELIC, autosomal or pseudoautosomal

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

SPTLC1 was added to Undiagnosed metabolic disorderspanel. Sources: Literature

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

SPTLC1 was created by sleigh