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FLASH GENE
Symbol SPTLC1 contributors: mct - updated : 22-12-2016
HGNC name serine palmitoyltransferase, long chain base subunit 1
HGNC id 11277
Corresponding disease
HSAN1 hereditary sensory and autonomic neuropathy, type 1
Location 9q22.31      Physical location : 94.793.426 - 94.877.690
Synonym name
  • serine-palmitoyl-CoA transferase 1
  • long chain base biosynthesis protein 1
  • Synonym symbol(s) LBC1, SPT1, HSN1, LCB1, MGC14645, SPTI
    EC.number 2.3.1.50
    DNA
    TYPE functioning gene
    STRUCTURE 84.26 kb     15 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status provisional
    Map cen - D9S1841 - ROR2 - SPTLC1 - OGN - ECM2 - OMD OMD - FGD3 - NINJ1 - D9S197 - qter
    Physical map
    AUH 9q22 AU RNA binding protein/enoyl-Coenzyme A hydratase NFIL3 9q22 nuclear factor, interleukin 3 regulated ROR2 9q22.3 receptor tyrosine kinase-like orphan receptor 2 LOC347318 9q22.31 similar to 60S ribosomal protein L21 SPTLC1 9q22.1-q22.2 serine palmitoyltransferase, long chain base subunit 1 LOC389772 9 similar to Osteotesticular phosphatase; protein tyrosine phosphatase, receptor type, V LOC392368 9 similar to KIAA1553 protein LOC138652 9q22.32 similar to bA62C3.1 (similar to testicular serine protease) IARS 9q21 isoleucine-tRNA synthetase C9orf34 9q22.32 chromosome 9 open reading frame 34 OGN 9q22.3 osteoglycin (osteoinductive factor, mimecan) OMD 9p22.3 osteomodulin ASPN 9q22-q31 asporin (LRR class 1) ECM2 9q22.3 extracellular matrix protein 2, female organ and adipocyte specific C9orf12 9q21.33-q22.31 chromosome 9 open reading frame 12 BICD2 9q22.1-q22.3 chromosome 9 open reading frame 12 ANKRD19 9q22.32 ankyrin repeat domain 19 BA526D8.4 9q22.32 KRAB box containing C2H2 type zinc finger bA526D8.4 LOC389773 9 LOC389773 LOC340518 9q22.32 similar to Alox15 protein FGD3 9q22 FGD1 family, member 3 MGC26847 LOC389774 9 LOC389774 MGC11115 9q22.32 hypothetical protein MGC11115 LOC389775 9 LOC389775 NINJ1 9q22.3 ninjurin 1
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    15 - 2780 - 473 - 2005 16210380
    6 - 998 - 143 - 2005 16210380
    EXPRESSION
    Type ubiquitous
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestiveintestinelarge intestinecolon highly
    Endocrineneuroendocrinepituitary  highly
    Lymphoid/Immunespleen   highly
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Nervousperipherous   
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • extracellular N and C termini
  • two transmembrane segments in the N terminal region,
  • several myristoylation sites
  • a putative glycosylation site
  • HOMOLOGY
    Homologene
    FAMILY
  • class-II pyridoxal-phosphate-dependent aminotransferase family
  • CATEGORY enzyme
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endoplasmic reticulum
    intracellular,nucleus
    text in addition to its "traditional" localization in the ER for de novo sphingolipid biosynthesis, is present in other cellular compartments, including focal adhesions where it is associated with cell morphology
    basic FUNCTION
  • initial step in sphingolipid biosynthesis, key enzyme for regulating cellular sphingolipid content
  • binds PARD3 that modulates monocyte serine palmitoyltransferase activity and chemotaxis
  • inhibits ABCA1 activity leading to the blockade of the exit of ABCA1 from the endoplasmic reticulum
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism lipid/lipoprotein
    signaling
    a component
    INTERACTION
    DNA
    RNA
    small molecule cofactor,
  • pyridoxal 5'-phosphate
  • protein
  • protein-protein interaction between SPTLC1 and the PDZ protein PARD3 (is able to associate with the SPTLC1/2 holoenzyme by binding the C-terminal SPTLC1 PDZ motif)
  • interacting with ABCA1 (inhibition of ABCA1 activity led to the blockade of the exit of ABCA1 from the endoplasmic reticulum)
  • physical interaction of ABCA1 and SPTLC1 results in reduction of ABCA1 activity and inhibition of this interaction produces enhanced cholesterol efflux
  • SPTSSA, SPTSSB share a conserved hydrophobic central domain predicted to reside in the membrane, and each interacts with both SPTLC1 and SPTLC2
  • SPTLC1 activity indirectly regulates ORMDL1, ORMDL2, ORMDL3 expression 2)
  • ORMDL3 might influence de novo sphingolipid metabolism downstream of SPTLC1
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) HSAN1
    related resource Mutation Database of Inherited Peripheral Neuropathies
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    SystemTypeDisorderPubmed
    neurologyneurodegenerativealzheimer
    SPTLC1, SPTLC2, SPTLC3 and MIR137 may be potential therapeutic targets for sporadic Alzheimer disease
    ANIMAL & CELL MODELS