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Inborn errors of metabolism

Gene: SPTLC2

Green List (high evidence)

SPTLC2 (serine palmitoyltransferase long chain base subunit 2)
EnsemblGeneIds (GRCh38): ENSG00000100596
EnsemblGeneIds (GRCh37): ENSG00000100596
OMIM: 605713, Gene2Phenotype
SPTLC2 is in 12 panels

2 reviews

Catherine Snow (Genomics England)

Green List (high evidence)

Promoted from Amber to Green. This gene is associated with a relevant disease on OMIM and Gene2Phenotype and there is enough evidence to support a gene-disease association.

SPTLC2, 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: 20920666 reports on three heterozygous missense mutations in the SPTLC2 subunit of SPT in four families and also confirmed cases in Bristol (see review on Hereditary Neuropathy panel https://panelapp.genomicsengland.co.uk/panels/85/).

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, 8:41 a.m. | Last Modified: 26 Sep 2019, 8:41 a.m.
Panel Version: 1.281

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

Phenotypes
Neuropathy, hereditary sensory and autonomic, type IC, 613640

Publications

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
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
605713
Clinvar variants
Variants in SPTLC2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

26 Sep 2019, Gel status: 3

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: sptlc2 has been classified as Green List (High Evidence).

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC2 were set to 27604308; 20920666

26 Sep 2019, Gel status: 2

Set publications

Catherine Snow (Genomics England)

Publications for gene: SPTLC2 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 SPTLC2. Source London North GLH was added to SPTLC2.

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: SPTLC2 was added gene: SPTLC2 was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: SPTLC2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SPTLC2 were set to 27604308 Phenotypes for gene: SPTLC2 were set to Charcot-Marie-Tooth disease; Serine palmitoyl transferase deficiency (Disorders of complex lipid synthesis); Familial dysautonomia