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FLASH GENE
Symbol SPTLC2 contributors: mct - updated : 22-12-2016
HGNC name serine palmitoyltransferase, long chain base subunit 2
HGNC id 11278
Corresponding disease
HSAN6 hereditary sensory and autonomic neuropathy, type VI
Location 14q24.3      Physical location : 77.973.271 - 78.083.110
Synonym name long chain base biosynthesis protein 2a
Synonym symbol(s) LBC2, KIAA0526, SPT2, LCB2A
EC.number 2.3.1.50
DNA
TYPE functioning gene
STRUCTURE 109.84 kb     12 Exon(s)
10 Kb 5' upstream gene genomic sequence study
regulatory sequence cytosine-phosphate-guanine/HTF
text structure
  • proximal 335 bp contain initiator and downstream promoter elements, two proximal GC boxes that appear to stimulate transcription in a cooperative manner, and several additional elements whose activity cannot be accounted for by known factor binding sites
  • MAPPING cloned Y linked N status provisional
    Physical map
    CYCSP1 14q24.3 cytochrome c, somatic pseudogene 1 LAMR1P3 14 laminin receptor 1 pseudogene 3 LOC388000 14 LOC388000 KIAA1036 14q24.3 LOC388000 KIAA0759 14q24.3 LOC388000 LOC145497 14q24.3 hypothetical protein LOC145497 RPL22P2 14 ribosomal protein L22 pseudogene 2 RPLP1P1 14q23 ribosomal protein, large, P1 pseudogene 1 C14orf4 14q24.3 chromosome 14 open reading frame 4 KIAA1737 14q24.3 KIAA1737 C14orf59 14 chromosome 14 open reading frame 59 C14orf171 14q24.3 chromosome 14 open reading frame 171 NGB 14q24 neuroglobin POMT2 14q24.3 protein-O-mannosyltransferase 2 GSTZ1 14q24.3 glutathione transferase zeta 1 (maleylacetoacetate isomerase) LOC283578 14q24.3 hypothetical protein LOC283578 LOC161394 14q24.3 hypothetical protein LOC161394 LOC122945 14q24.3 hypothetical protein FLJ32809 C14orf133 14q24.3-q31 chromosome 14 open reading frame 133 AHSA1 14q23.3-31 AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) THSD3 14q24.3 thrombospondin, type I domain-containing 3 SPTLC2 14q24.3-q31 serine palmitoyltransferase, long chain base subunit 2 ALKBH 14q24 alkB, alkylation repair homolog (E. coli) RPL21P10 14 ribosomal protein L21 pseudogene 10 DC50 14q24.3 hypothetical protein DC50 SNW1 14q24.3 hypothetical protein DC50 FLJ25976 14q24.3 hypothetical protein FLJ25976 ADCK1 14q24.3 aarF domain containing kinase 1 FRDAP 14q24.3 Friedreich ataxia pseudogene
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    12 - 7250 62.9 562 - 2010 20920666
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivestomach    
    Lymphoid/Immunelymph node    
     spleen    
    Reproductivefemale systembreastmammary gland  
     female systemuterus   
    Respiratoryrespiratory tractlarynx  highly
    Urinarykidney    
    cell lineage
    cell lines
    fluid/secretion blood
    at STAGE
    physiological period pregnancy
    Text placenta
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • a peptide sequence motif, signature of Lc62 proteins
  • also part of the catalytic domain
  • HOMOLOGY
    interspecies ortholog to murine Sptlc2
    Homologene
    FAMILY
  • aminolevulinate synthetase superfamily
  • class-II pyridoxal-phosphate-dependent aminotransferase family
  • CATEGORY enzyme
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm,organelle,mitochondria
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endoplasmic reticulum
    basic FUNCTION
  • initial step in sphingolipid biosynthesis, key enzyme for regulating cellular sphingolipid content
  • catalyzes the first and rate-limiting step in the de novo sphingolipid synthesis pathway
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism lipid/lipoprotein
    signaling
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
  • SPTSSA, SPTSSB share a conserved hydrophobic central domain predicted to reside in the membrane, and each interacts with both SPTLC1 and SPTLC2
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) HSAN6
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional       loss of function
    deficiency of SPTLC2 induces necrotic lesions in gastrointestinal cells followed by atrophic change of the tissue in short term
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • plasma from Sptlc2 knock-out mice had a significantly stronger potential for promoting cholesterol efflux from macrophages than from wild-type mice because of a greater amount of apoE in the circulation