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Aliases for SPTLC2 Gene

Aliases for SPTLC2 Gene

  • Serine Palmitoyltransferase, Long Chain Base Subunit 2 2 3
  • LCB2 3 4 6
  • Long Chain Base Biosynthesis Protein 2a 3 4
  • Serine-Palmitoyl-CoA Transferase 2 3 4
  • EC 4 64
  • KIAA0526 4 6
  • NSAN1C 3 6
  • LCB 2 3 4
  • SPT 2 3 4
  • LCB2A 3 4
  • HSN1C 3 6
  • SPT2 3 6
  • Serine Palmitoyltransferase, Subunit II 3
  • Long Chain Base Biosynthesis Protein 2 4
  • Serine Palmitoyltransferase 2 3
  • EC 2.3.1 64
  • HLCB2a 3

External Ids for SPTLC2 Gene

Summaries for SPTLC2 Gene

Entrez Gene Summary for SPTLC2 Gene

  • This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011]

GeneCards Summary for SPTLC2 Gene

SPTLC2 (Serine Palmitoyltransferase, Long Chain Base Subunit 2) is a Protein Coding gene. Diseases associated with SPTLC2 include neuropathy, hereditary sensory and autonomic, type ic 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. An important paralog of this gene is SPTLC3.

UniProtKB/Swiss-Prot for SPTLC2 Gene

  • Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 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-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.

Gene Wiki entry for SPTLC2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPTLC2 Gene

Genomics for SPTLC2 Gene

Genomic Location for SPTLC2 Gene

77,505,997 bp from pter
77,616,773 bp from pter
110,777 bases
Minus strand

Genomic View for SPTLC2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SPTLC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTLC2 Gene

Regulatory Elements for SPTLC2 Gene

Proteins for SPTLC2 Gene

  • Protein details for SPTLC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Serine palmitoyltransferase 2
    Protein Accession:
    Secondary Accessions:
    • Q16685

    Protein attributes for SPTLC2 Gene

    562 amino acids
    Molecular mass:
    62924 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Heterodimer with SPTLC1. Component of the serine palmitoyltransferase (SPT) complex, composed of LCB1/SPTLC1, LCB2 (SPTLC2 or SPTLC3) and ssPT (SPTSSA and SPTSSB).
    • Sequence=BAA25452.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SPTLC2 Gene

Proteomics data for SPTLC2 Gene at MOPED

Post-translational modifications for SPTLC2 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys161

Other Protein References for SPTLC2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for SPTLC2 Gene


  • Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.:
    • O15270
genes like me logo Genes that share domains with SPTLC2: view

No data available for Gene Families for SPTLC2 Gene

Function for SPTLC2 Gene

Molecular function for SPTLC2 Gene

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 LCB1/SPTLC1 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-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.

Enzyme Numbers (IUBMB) for SPTLC2 Gene

Gene Ontology (GO) - Molecular Function for SPTLC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004758 serine C-palmitoyltransferase activity IDA 19416851
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with SPTLC2: view
genes like me logo Genes that share phenotypes with SPTLC2: view

Animal Models for SPTLC2 Gene

MGI Knock Outs for SPTLC2:

No data available for miRNA , Transcription Factor Targeting and HOMER Transcription for SPTLC2 Gene

Localization for SPTLC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTLC2 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein.

Subcellular locations from

Jensen Localization Image for SPTLC2 Gene COMPARTMENTS Subcellular localization image for SPTLC2 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 3
cytosol 2
extracellular 1
nucleus 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SPTLC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IDA 19416851
genes like me logo Genes that share ontologies with SPTLC2: view

Pathways for SPTLC2 Gene

genes like me logo Genes that share pathways with SPTLC2: view

Pathways by source for SPTLC2 Gene

UniProtKB/Swiss-Prot O15270-SPTC2_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism

Gene Ontology (GO) - Biological Process for SPTLC2 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 SPTLC2: view

Compounds for SPTLC2 Gene

(6) HMDB Compounds for SPTLC2 Gene

Compound Synonyms Cas Number PubMed IDs
  • 1-Hydroxy-2-amino-3-oxo-octadecane
Carbon dioxide
  • Carbon oxide
Coenzyme A
  • Acetoacetyl coenzyme A sodium salt
  • (-)-Serine
  • Palmityl-CoA

(2) Drugbank Compounds for SPTLC2 Gene

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

(3) Novoseek inferred chemical compound relationships for SPTLC2 Gene

Compound -log(P) Hits PubMed IDs
glucosylceramide 73.8 1
serine 71.1 7
ceramide 69.8 2
genes like me logo Genes that share compounds with SPTLC2: view

Transcripts for SPTLC2 Gene

mRNA/cDNA for SPTLC2 Gene

Unigene Clusters for SPTLC2 Gene

Serine palmitoyltransferase, long chain base subunit 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC2 Gene

No ASD Table

Relevant External Links for SPTLC2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SPTLC2 Gene

mRNA expression in normal human tissues for SPTLC2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPTLC2 Gene

This gene is overexpressed in Whole Blood (6.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SPTLC2 Gene

SOURCE GeneReport for Unigene cluster for SPTLC2 Gene Hs.435661

mRNA Expression by UniProt/SwissProt for SPTLC2 Gene

Tissue specificity: Widely expressed.
genes like me logo Genes that share expressions with SPTLC2: view

Orthologs for SPTLC2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPTLC2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SPTLC2 36
  • 99.58 (n)
  • 100 (a)
  • 100 (a)
(Bos Taurus)
Mammalia SPTLC2 36
  • 90.73 (n)
  • 95.01 (a)
  • 95 (a)
(Canis familiaris)
Mammalia SPTLC2 36
  • 92.35 (n)
  • 96.8 (a)
  • 97 (a)
(Mus musculus)
Mammalia Sptlc2 36
  • 90.83 (n)
  • 96.43 (a)
Sptlc2 16
Sptlc2 37
  • 96 (a)
(Monodelphis domestica)
Mammalia SPTLC2 37
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia SPTLC2 37
  • 81 (a)
(Rattus norvegicus)
Mammalia Sptlc2 36
  • 89.64 (n)
  • 95.71 (a)
(Gallus gallus)
Aves SPTLC2 36
  • 79.5 (n)
  • 89.21 (a)
  • 86 (a)
(Anolis carolinensis)
Reptilia SPTLC2 37
  • 88 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2338 36
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc2 36
  • 73.54 (n)
  • 86.77 (a)
(Danio rerio)
Actinopterygii Dr.16885 36
sptlc2a 36
  • 72.45 (n)
  • 81.89 (a)
sptlc2a 37
  • 77 (a)
sptlc2b 37
  • 75 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007941 36
  • 59.28 (n)
  • 58.23 (a)
fruit fly
(Drosophila melanogaster)
Insecta lace 36
  • 59 (n)
  • 57.53 (a)
lace 37
  • 47 (a)
lace 38
  • 56 (a)
(Caenorhabditis elegans)
Secernentea sptl-2 36
  • 57.79 (n)
  • 55.33 (a)
sptl-2 37
  • 45 (a)
sptl-3 37
  • 45 (a)
F43H9.2b 38
  • 55 (a)
T22G5.5 38
  • 49 (a)
F43H9.2a 38
  • 55 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR127C 36
  • 52.73 (n)
  • 47.95 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB2 36
  • 53.31 (n)
  • 48.47 (a)
LCB2 37
  • 43 (a)
LCB2 39
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D02134g 36
  • 53.42 (n)
  • 47.86 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2016 36
thale cress
(Arabidopsis thaliana)
eudicotyledons LCB2 36
  • 56.59 (n)
  • 53.56 (a)
(Hordeum vulgare)
Liliopsida Hv.11007 36
(Zea mays)
Liliopsida Zm.13752 36
(Oryza sativa)
Liliopsida Os01g0928800 36
  • 56.82 (n)
  • 53.96 (a)
(Triticum aestivum)
Liliopsida Ta.2702 36
bread mold
(Neurospora crassa)
Ascomycetes NCU00447 36
  • 55.24 (n)
  • 51.75 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lcb2 36
  • 52.82 (n)
  • 50.42 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.835 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 56 (a)
Species with no ortholog for SPTLC2:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for SPTLC2 Gene

Gene Tree for SPTLC2 (if available)
Gene Tree for SPTLC2 (if available)

Paralogs for SPTLC2 Gene

Paralogs for SPTLC2 Gene

Selected SIMAP similar genes for SPTLC2 Gene using alignment to 4 proteins: Pseudogenes for SPTLC2 Gene

genes like me logo Genes that share paralogs with SPTLC2: view

Variants for SPTLC2 Gene

Sequence variations from dbSNP and Humsavar for SPTLC2 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs3101 -- 77,535,654(-) CCATG(C/T)TGGTC intron-variant
rs13430 -- 77,506,889(-) TGAAG(C/G)AATAC utr-variant-3-prime
rs176894 -- 77,608,274(+) GGCTA(C/T)GGGTT intron-variant
rs176895 -- 77,608,463(+) GCTTA(C/T)ATGCT intron-variant
rs176896 -- 77,608,597(+) GATAA(A/G)CAAAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SPTLC2 Gene

Variant ID Type Subtype PubMed ID
nsv832835 CNV Gain 17160897
nsv85432 CNV Loss 16902084
esv274095 CNV Insertion 20981092
esv7096 OTHER Inversion 19470904
esv267469 CNV Insertion 20981092
dgv643e1 CNV Complex 17122850

Relevant External Links for SPTLC2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

Disorders for SPTLC2 Gene

(1) OMIM Diseases for SPTLC2 Gene (605713)


  • Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C) [MIM:613640]: 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. HSAN1C symptoms include loss of touch and vibration in the feet, dysesthesia and severe panmodal sensory loss in the upper and lower limbs, distal lower limb sensory loss with ulceration and osteomyelitis, and distal muscle weakness. {ECO:0000269 PubMed:20920666, ECO:0000269 PubMed:23658386}. Note=The disease is caused by mutations affecting the gene represented in this entry. SPTLC2 disease mutations cause a shift in the substrate specificity of SPT resulting in the alternative use of L-alanine and L-glycine over its canonical substrate L-serine. This leads to the production of 1-deoxysphingolipids that cannot be correctly metabolized (PubMed:23658386). {ECO:0000269 PubMed:23658386}.

(1) University of Copenhagen DISEASES for SPTLC2 Gene

(2) Novoseek inferred disease relationships for SPTLC2 Gene

Disease -log(P) Hits PubMed IDs
neuropathy, hereditary sensory, type i 90.9 1
sensory neuropathy hereditary 86.5 1

Relevant External Links for SPTLC2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SPTLC2: view

Publications for SPTLC2 Gene

  1. Sphingolipid synthesis: identification and characterization of mammalian cDNAs encoding the Lcb2 subunit of serine palmitoyltransferase. (PMID: 8921873) Nagiec M.M. … Dickson R.C. (Gene 1996) 2 3 4 23
  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 3 4 23
  3. Exclusion of serine palmitoyltransferase long chain base subunit 2 (SPTLC2) as a common cause for hereditary sensory neuropathy. (PMID: 12207934) Dawkins J.L. … Nicholson G.A. (Neuromuscul. Disord. 2002) 3 23
  4. Permeability barrier disruption increases the level of serine palmitoyltransferase in human epidermis. (PMID: 12445191) Stachowitz S. … Behrendt H. (J. Invest. Dermatol. 2002) 3 23
  5. Is the mammalian serine palmitoyltransferase a high-molecular-mass complex? (PMID: 17331073) Hornemann T. … von Eckardstein A. (Biochem. J. 2007) 3 23

Products for SPTLC2 Gene

Sources for SPTLC2 Gene

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