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Aliases for SPTLC1 Gene

Aliases for SPTLC1 Gene

  • Serine Palmitoyltransferase, Long Chain Base Subunit 1 2 3
  • SPT1 3 4 6
  • Long Chain Base Biosynthesis Protein 1 3 4
  • Serine-Palmitoyl-CoA Transferase 1 3 4
  • EC 2.3.1.50 4 63
  • LCB 1 3 4
  • SPT 1 3 4
  • LBC1 3 6
  • HSN1 3 6
  • LCB1 3 4
  • Hereditary Sensory Neuropathy, Type 1 2
  • Serine C-Palmitoyltransferase 3
  • Serine Palmitoyltransferase 1 3
  • HSAN1 3
  • HSAN 6
  • SPTI 3

External Ids for SPTLC1 Gene

Previous Symbols for SPTLC1 Gene

  • HSN1

Summaries for SPTLC1 Gene

Entrez Gene Summary for SPTLC1 Gene

  • This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]

GeneCards Summary for SPTLC1 Gene

SPTLC1 (Serine Palmitoyltransferase, Long Chain Base Subunit 1) is a Protein Coding gene. Diseases associated with SPTLC1 include neuropathy, hereditary sensory and autonomic, type ia and hereditary sensory neuropathy. Among its related pathways are Sphingolipid metabolism and Sphingolipid metabolism. GO annotations related to this gene include pyridoxal phosphate binding and serine C-palmitoyltransferase activity.

UniProtKB/Swiss-Prot for SPTLC1 Gene

  • Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference.

Gene Wiki entry for SPTLC1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPTLC1 Gene

Genomics for SPTLC1 Gene

Genomic Location for SPTLC1 Gene

Start:
92,031,134 bp from pter
End:
92,115,474 bp from pter
Size:
84,341 bases
Orientation:
Minus strand

Genomic View for SPTLC1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SPTLC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTLC1 Gene

Regulatory Elements for SPTLC1 Gene

Proteins for SPTLC1 Gene

  • Protein details for SPTLC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15269-SPTC1_HUMAN
    Recommended name:
    Serine palmitoyltransferase 1
    Protein Accession:
    O15269
    Secondary Accessions:
    • A8K681
    • Q5VWB4
    • Q96IX6

    Protein attributes for SPTLC1 Gene

    Size:
    473 amino acids
    Molecular mass:
    52744 Da
    Cofactor:
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Heterodimer with SPTLC2 or SPTLC3. Component of the serine palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB. Interacts with SPTSSA and SPTSSB; the interaction is direct. Interacts with ORMDL3.

    Alternative splice isoforms for SPTLC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTLC1 Gene

Proteomics data for SPTLC1 Gene at MOPED

Post-translational modifications for SPTLC1 Gene

  • Phosphorylation at Tyr-164 inhibits activity and promotes cell survival.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys57, Lys197, and Lys375

Other Protein References for SPTLC1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for SPTLC1 Gene

Suggested Antigen Peptide Sequences for SPTLC1 Gene

Graphical View of Domain Structure for InterPro Entry

O15269

UniProtKB/Swiss-Prot:

SPTC1_HUMAN
Family:
  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.:
    • O15269
genes like me logo Genes that share domains with SPTLC1: view

No data available for Gene Families for SPTLC1 Gene

Function for SPTLC1 Gene

Molecular function for SPTLC1 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=0.75 mM for serine {ECO:0000269 PubMed:20504773}; Vmax=1350 pmol/min/mg enzyme {ECO:0000269 PubMed:20504773};
UniProtKB/Swiss-Prot CatalyticActivity: Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2).
UniProtKB/Swiss-Prot Function: Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference.

Enzyme Numbers (IUBMB) for SPTLC1 Gene

Gene Ontology (GO) - Molecular Function for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004758 serine C-palmitoyltransferase activity IDA 19416851
GO:0005515 protein binding IPI 19416851
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with SPTLC1: view
genes like me logo Genes that share phenotypes with SPTLC1: view

Animal Models for SPTLC1 Gene

MGI Knock Outs for SPTLC1:

miRNA for SPTLC1 Gene

No data available for Transcription Factor Targeting and HOMER Transcription for SPTLC1 Gene

Localization for SPTLC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTLC1 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SPTLC1 Gene COMPARTMENTS Subcellular localization image for SPTLC1 gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 2
extracellular 1
golgi apparatus 1
mitochondrion 1
nucleus 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IDA 19416851
GO:0035339 SPOTS complex IDA 20182505
genes like me logo Genes that share ontologies with SPTLC1: view

Pathways for SPTLC1 Gene

genes like me logo Genes that share pathways with SPTLC1: view

Pathways by source for SPTLC1 Gene

UniProtKB/Swiss-Prot O15269-SPTC1_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism

Gene Ontology (GO) - Biological Process for SPTLC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006665 sphingolipid metabolic process TAS --
GO:0006686 sphingomyelin biosynthetic process IEA --
GO:0009058 biosynthetic process --
GO:0030148 sphingolipid biosynthetic process TAS 19416851
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with SPTLC1: view

Compounds for SPTLC1 Gene

(8) HMDB Compounds for SPTLC1 Gene

Compound Synonyms Cas Number PubMed IDs
3-Dehydrosphinganine
  • 1-Hydroxy-2-amino-3-oxo-octadecane
16105-69-4
Alpha-Tocopherol
  • Vitamin Ea
59-02-9
Carbon dioxide
  • Carbon oxide
124-38-9
Coenzyme A
  • Acetoacetyl coenzyme A sodium salt
85-61-0
L-Serine
  • (-)-Serine
56-45-1

(2) Drugbank Compounds for SPTLC1 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
L-Serine
  • (-)-Serine
56-45-1 target
Pyridoxal Phosphate
  • Codecarboxylase
54-47-7 target cofactor

(3) Novoseek inferred chemical compound relationships for SPTLC1 Gene

Compound -log(P) Hits PubMed IDs
serine 72.4 16
ceramide 63.6 3
cholesterol 2 3
genes like me logo Genes that share compounds with SPTLC1: view

Transcripts for SPTLC1 Gene

Unigene Clusters for SPTLC1 Gene

Serine palmitoyltransferase, long chain base subunit 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC1 Gene

No ASD Table

Relevant External Links for SPTLC1 Gene

GeneLoc Exon Structure for
SPTLC1
ECgene alternative splicing isoforms for
SPTLC1

Expression for SPTLC1 Gene

mRNA expression in normal human tissues for SPTLC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SPTLC1 Gene

SOURCE GeneReport for Unigene cluster for SPTLC1 Gene Hs.90458

mRNA Expression by UniProt/SwissProt for SPTLC1 Gene

O15269-SPTC1_HUMAN
Tissue specificity: Widely expressed. Not detected in small intestine.
genes like me logo Genes that share expressions with SPTLC1: view

No data available for mRNA differential expression in normal tissues for SPTLC1 Gene

Orthologs for SPTLC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPTLC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPTLC1 35
  • 99.4 (n)
  • 99.1 (a)
SPTLC1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SPTLC1 35
  • 91.68 (n)
  • 93.02 (a)
SPTLC1 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SPTLC1 35
  • 91.97 (n)
  • 94.93 (a)
SPTLC1 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sptlc1 35
  • 84.57 (n)
  • 91.75 (a)
Sptlc1 16
Sptlc1 36
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SPTLC1 36
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptlc1 35
  • 84 (n)
  • 91.33 (a)
chicken
(Gallus gallus)
Aves SPTLC1 35
  • 79.8 (n)
  • 87.5 (a)
SPTLC1 36
  • 86 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPTLC1 36
  • 87 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7364 35
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc1 35
  • 76.86 (n)
  • 87.26 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9491 35
zebrafish
(Danio rerio)
Actinopterygii -- 35
sptlc1 35
  • 72.45 (n)
  • 84.8 (a)
sptlc1 36
  • 82 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010427 35
  • 53.52 (n)
  • 53.59 (a)
fruit fly
(Drosophila melanogaster)
Insecta Spt-I 35
  • 54.4 (n)
  • 52.59 (a)
Spt-I 36
  • 50 (a)
OneToOne
Spt-I 37
  • 52 (a)
worm
(Caenorhabditis elegans)
Secernentea sptl-1 35
  • 57.06 (n)
  • 53.27 (a)
sptl-1 36
  • 48 (a)
OneToOne
C23H3.4 37
  • 49 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR145C 35
  • 45.52 (n)
  • 39.95 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB1 35
  • 47.12 (n)
  • 37.98 (a)
LCB1 36
  • 29 (a)
OneToOne
LCB1 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A09955g 35
  • 46.28 (n)
  • 40.05 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons LCB1 35
  • 52.49 (n)
  • 45.02 (a)
rice
(Oryza sativa)
Liliopsida Os02g0806900 35
  • 53.75 (n)
  • 48.55 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06870 35
  • 46.73 (n)
  • 39.95 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC18E5.02c 35
  • 49.88 (n)
  • 42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 56 (a)
OneToMany
-- 36
  • 61 (a)
OneToMany
Species with no ortholog for SPTLC1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SPTLC1 Gene

ENSEMBL:
Gene Tree for SPTLC1 (if available)
TreeFam:
Gene Tree for SPTLC1 (if available)

Paralogs for SPTLC1 Gene

genes like me logo Genes that share paralogs with SPTLC1: view

No data available for Paralogs for SPTLC1 Gene

Variants for SPTLC1 Gene

Sequence variations from dbSNP and Humsavar for SPTLC1 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs7944 -- 92,032,020(+) ATATG(C/T)TGAAG utr-variant-3-prime
rs1131864 -- 92,032,387(-) GTGGC(C/T)TGAAA reference, synonymous-codon, utr-variant-3-prime
rs1131866 -- 92,032,363(-) TGTGG(A/G)TCTTT reference, missense, utr-variant-3-prime
rs1135523 -- 92,079,240(-) aaatt(A/G)gctgg intron-variant, utr-variant-3-prime
rs1135524 -- 92,079,220(-) tggat(A/G)cctgt intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SPTLC1 Gene

Variant ID Type Subtype PubMed ID
nsv831653 CNV Gain 17160897

Relevant External Links for SPTLC1 Gene

HapMap Linkage Disequilibrium report
SPTLC1
Human Gene Mutation Database (HGMD)
SPTLC1
Locus Specific Mutation Databases (LSDB)
SPTLC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC1 Gene

Disorders for SPTLC1 Gene

(1) OMIM Diseases for SPTLC1 Gene (605712)

UniProtKB/Swiss-Prot

SPTC1_HUMAN
  • Neuropathy, hereditary sensory and autonomic, 1A (HSAN1A) [MIM:162400]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections, osteomyelitis, and amputations. HSAN1A is an autosomal dominant axonal form with onset in the second or third decades. Initial symptoms are loss of pain, touch, heat, and cold sensation over the feet, followed by distal muscle wasting and weakness. Loss of pain sensation leads to chronic skin ulcers and distal amputations. {ECO:0000269 PubMed:11242114, ECO:0000269 PubMed:19651702, ECO:0000269 PubMed:21618344, ECO:0000269 PubMed:22302274}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for SPTLC1 Gene

(5) Novoseek inferred disease relationships for SPTLC1 Gene

Disease -log(P) Hits PubMed IDs
neuropathy, hereditary sensory, type i 97.5 8
sensory neuropathy hereditary 92.6 1
sensory neuropathy 69.6 1
charcot-marie-tooth disease 66.3 1
neurodegeneration 34.7 1

Relevant External Links for SPTLC1

GeneTests
SPTLC1
GeneReviews
SPTLC1
Genetic Association Database (GAD)
SPTLC1
Human Genome Epidemiology (HuGE) Navigator
SPTLC1
genes like me logo Genes that share disorders with SPTLC1: view

Publications for SPTLC1 Gene

  1. Human and murine serine-palmitoyl-CoA transferase. Cloning, expression and characterization of the key enzyme in sphingolipid synthesis. (PMID: 9363775) Weiss B. … Stoffel W. (Eur. J. Biochem. 1997) 2 3 4 23
  2. Genes for hereditary sensory and autonomic neuropathies: a genotype- phenotype correlation. (PMID: 19651702) Rotthier A. … Timmerman V. (Brain 2009) 3 4 23 48
  3. Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I. (PMID: 11242114) Dawkins J.L. … Nicholson G.A. (Nat. Genet. 2001) 3 4 23
  4. SPTLC1 mutation in twin sisters with hereditary sensory neuropathy type I. (PMID: 15037712) Verhoeven K. … De Jonghe P. (Neurology 2004) 3 4 23
  5. Hereditary sensory neuropathy type I: haplotype analysis shows founders in southern England and Europe. (PMID: 11479835) Nicholson G.A. … Hulme D.J. (Am. J. Hum. Genet. 2001) 3 23

Products for SPTLC1 Gene

Sources for SPTLC1 Gene

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