Likely inborn error of metabolism - targeted testing not possible
Gene: SPTLC1The 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
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
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 imprintedCreated: 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
Tag Q1_22_MOI was removed from gene: SPTLC1.
Mode of inheritance for gene SPTLC1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Tag Q1_22_MOI tag was added to gene: SPTLC1.
Mode of inheritance for gene: SPTLC1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926
Gene: sptlc1 has been classified as Green List (High Evidence).
Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926
Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926
Publications for gene: SPTLC1 were set to 27604308; 20097765; 21618344; 20097765; 30420926
Publications for gene: SPTLC1 were set to 27604308
Source NHS GMS was added to SPTLC1. Source London North GLH was added to SPTLC1.
Sarah Leigh: Associated with relevant pheno
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