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Aliases for SPTLC1 Gene

Aliases for SPTLC1 Gene

  • Serine Palmitoyltransferase, Long Chain Base Subunit 1 2 3
  • 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
  • LCB1 3 4
  • SPT1 3 4
  • Hereditary Sensory Neuropathy, Type 1 2
  • Serine C-Palmitoyltransferase 3
  • HSAN1 3
  • LBC1 3
  • SPTI 3
  • HSN1 3

External Ids for SPTLC1 Gene

Previous HGNC Symbols for SPTLC1 Gene

  • HSN1

Previous GeneCards Identifiers for SPTLC1 Gene

  • GC09M085621
  • GC09M086522
  • GC09M088092
  • GC09M090134
  • GC09M091873
  • GC09M093833
  • GC09M094793
  • GC09M064471

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 dnmt1-related dementia, deafness, and sensory neuropathy. Among its related pathways are 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

Regulatory Elements for SPTLC1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SPTLC1 Gene

Chromosome:
9
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

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.
  • Ubiquitination at Lys 57, Lys 197, and Lys 375
  • Modification sites at PhosphoSitePlus

Other Protein References for SPTLC1 Gene

Antibody Products

Domains & Families for SPTLC1 Gene

Suggested Antigen Peptide Sequences for SPTLC1 Gene

Graphical View of Domain Structure for InterPro Entry

O15269

UniProtKB/Swiss-Prot:

SPTC1_HUMAN :
  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Family:
  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
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:

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SPTLC1

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targets 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 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 & Interactions 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

SIGNOR curated interactions for SPTLC1 Gene

Is inactivated by:

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

Drugs & Compounds for SPTLC1 Gene

(7) Drugs for SPTLC1 Gene - From: HMDB, DrugBank, NovoSeek, and DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Serine Approved Nutra Full agonist, Agonist, Target Weak endogenous glycine receptor agonist 0
Vitamin E Approved Nutra 350,355
cholesterol Experimental Pharma Agonist 0
Pyridoxal Phosphate Nutra Target, cofactor 14
Myriocin Pharma 0

(6) Additional Compounds for SPTLC1 Gene - From: HMDB and NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Dehydrosphinganine
  • (2S)-2-amino-1-hydroxyoctadecan-3-one
  • 1-Hydroxy-2-amino-3-oxo-octadecane
  • 2-Amino-1-hydroxy-3-Octadecanone
  • 3-Dehydro-D-sphinganine
  • 3-Dehydrosphinganine
16105-69-4
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
124-38-9
hexadecanoyl-CoA
Palmityl-CoA
  • Hexadecanoyl CoA
  • Hexadecanoyl Coenzyme A
  • Palmitoyl CoA
  • Palmitoyl coenzyme a
  • Palmitoyl-CoA
1763-10-6
squalene
  • (all-E)-2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-Tetracosahexaene
  • (E,E,E,E)-Squalene
  • 2,6,10,15,19,23-Hexamethyl-2,6,10,14,18,22-tetracosahexaene
  • All-trans-Squalene
  • Nikko Squalane EX
111-02-4
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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SPTLC1

Flow Cytometry Products

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

Protein differential expression in normal tissues from HIPED for SPTLC1 Gene

This gene is overexpressed in Bone (22.9) and Peripheral blood mononuclear cells (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with SPTLC1: view

Protein tissue co-expression partners for SPTLC1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and 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
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
chimpanzee
(Pan troglodytes)
Mammalia SPTLC1 35
  • 99.4 (n)
  • 99.1 (a)
SPTLC1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptlc1 35
  • 84 (n)
  • 91.33 (a)
oppossum
(Monodelphis domestica)
Mammalia SPTLC1 36
  • 83 (a)
OneToOne
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
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc1 35
  • 76.86 (n)
  • 87.26 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7364 35
zebrafish
(Danio rerio)
Actinopterygii -- 35
sptlc1 35
  • 72.45 (n)
  • 84.8 (a)
sptlc1 36
  • 82 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9491 35
fruit fly
(Drosophila melanogaster)
Insecta Spt-I 37
  • 52 (a)
Spt-I 35
  • 54.4 (n)
  • 52.59 (a)
Spt-I 36
  • 50 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010427 35
  • 53.52 (n)
  • 53.59 (a)
worm
(Caenorhabditis elegans)
Secernentea C23H3.4 37
  • 49 (a)
sptl-1 35
  • 57.06 (n)
  • 53.27 (a)
sptl-1 36
  • 48 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR145C 35
  • 45.52 (n)
  • 39.95 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A09955g 35
  • 46.28 (n)
  • 40.05 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB1 35
  • 47.12 (n)
  • 37.98 (a)
LCB1 36
  • 29 (a)
OneToOne
LCB1 38
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
rs76163929 -- 92,046,404(+) AACTA(C/T)AGTAA intron-variant
rs76208582 -- 92,114,754(+) AAAAA(A/T)AAATA intron-variant
rs76273355 -- 92,046,229(+) GGTGC(G/T)TGCTA intron-variant, utr-variant-3-prime
rs76398660 -- 92,063,926(+) TAAAC(A/G)CTTTC intron-variant
rs76476269 -- 92,050,806(+) CACAA(C/T)ACTGA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv831653 CNV Gain 17160897

Variation tolerance for SPTLC1 Gene

Residual Variation Intolerance Score: 20.47% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.92; 48.92% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SPTLC1 Gene

HapMap Linkage Disequilibrium report
SPTLC1
Human Gene Mutation Database (HGMD)
SPTLC1

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

Disorders for SPTLC1 Gene

MalaCards: The human disease database

(22) MalaCards diseases for SPTLC1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory and autonomic, type ia
  • hereditary sensory neuropathy type ia
dnmt1-related dementia, deafness, and sensory neuropathy
  • hereditary sensoryautonomic neuropathy type 1 with dementiahearing loss
hereditary sensory neuropathy
  • hereditary sensory and autonomic neuropathy
sensory neuropathy type 1
lumbosacral lipoma
- elite association

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, ECO:0000269 PubMed:24247255}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=SPTLC1 mutations at Ser-331 are responsible for severe hereditary motor and sensory neuropathy (HMSN) forms, whose core features are severe, diffuse muscle wasting and hypotonia, motor and sensory disturbances, foot ulcers, amputations and/or burns, joint hypermobility, cataracts and considerable growth retardation. {ECO:0000269 PubMed:23454272}.

Relevant External Links for SPTLC1

Genetic Association Database (GAD)
SPTLC1
Human Genome Epidemiology (HuGE) Navigator
SPTLC1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SPTLC1
genes like me logo Genes that share disorders with SPTLC1: view

No data available for Genatlas for SPTLC1 Gene

Publications for SPTLC1 Gene

  1. Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase. (PMID: 11781309) Gable K. … Dunn T.M. (J. Biol. Chem. 2002) 23 25 67
  2. 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 23 67
  3. Effect of expression of genes in the sphingolipid synthesis pathway on the biosynthesis of ceramide in Saccharomyces cerevisiae. (PMID: 20208441) Kim S.K. … Yun H.S. (J. Microbiol. Biotechnol. 2010) 23 67
  4. Genes for hereditary sensory and autonomic neuropathies: a genotype- phenotype correlation. (PMID: 19651702) Rotthier A. … Timmerman V. (Brain 2009) 23 67
  5. Cell polarity factor Par3 binds SPTLC1 and modulates monocyte serine palmitoyltransferase activity and chemotaxis. (PMID: 19592499) Tamehiro N. … Fitzgerald M.L. (J. Biol. Chem. 2009) 23 67

Products for SPTLC1 Gene

Sources for SPTLC1 Gene

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