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Likely inborn error of metabolism

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 11 panels

3 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

The mode of inheritance of this gene has been updated to 'MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted' following NHS Genomic Medicine Service approval.
Created: 1 Feb 2023, 10:24 a.m. | Last Modified: 1 Feb 2023, 10:24 a.m.
Panel Version: 3.6
Created: 1 Feb 2023, 10:24 a.m.
Last Modified: 1 Feb 2023, 10:24 a.m.
Panel version: 3.6

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.

This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype.
Created: 26 Sep 2019, 9:42 a.m. | Last Modified: 26 Sep 2019, 9:55 a.m.
Panel Version: 1.286

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

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

Publications

Mode of pathogenicity
Other

Created: 26 Sep 2019, 9:42 a.m.
Last Modified: 26 Sep 2019, 9:55 a.m.
Panel version: 1.283

Sarah Leigh (Genomics England Curator)

Comment on mode of inheritance: There is no data to support that homozygous variants of SPTLC1 are associated with Neuropathy, hereditary sensory and autonomic, type IA, OMIM:162400. Therefore the MOI for this gene should be MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Created: 29 Mar 2022, 11:02 a.m. | Last Modified: 29 Mar 2022, 11:02 a.m.
Panel Version: 2.236
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.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Familial dysautonomia

Created: 6 Jan 2017, 2:03 p.m.

Panel version: Imported from Undiagnosed metabolic disorders panel version 0.15

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • London North GLH
  • NHS GMS
Phenotypes
  • Charcot-Marie-Tooth disease
  • Serine palmitoyl transferase deficiency (Disorders of complex lipid synthesis)
  • Familial dysautonomia
OMIM
605712
Clinvar variants
Variants in SPTLC1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Feb 2023, Gel status: 3

Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_22_MOI was removed from gene: SPTLC1.

1 Feb 2023, Gel status: 3

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene SPTLC1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

29 Mar 2022, Gel status: 3

Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q1_22_MOI tag was added to gene: SPTLC1.

29 Mar 2022, Gel status: 3

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

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

29 Mar 2022, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926

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).

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC1 were set to 27604308

13 Feb 2019, Gel status: 2

Added New Source, Added New Source

Ivone Leong (Genomics England Curator)

Source NHS GMS was added to SPTLC1. Source London North GLH was added to SPTLC1.

8 Jan 2019, Gel status: 2

Panel promoted to version 1.0

Ellen McDonagh (Genomics England Curator)

Sarah Leigh: Associated with relevant pheno

16 Dec 2018, Gel status: 2

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

Ellen McDonagh (Genomics England Curator)

gene: SPTLC1 was added gene: SPTLC1 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SPTLC1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: SPTLC1 were set to 27604308 Phenotypes for gene: SPTLC1 were set to Charcot-Marie-Tooth disease; Serine palmitoyl transferase deficiency (Disorders of complex lipid synthesis); Familial dysautonomia