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Aliases for SPTLC2 Gene

Aliases for SPTLC2 Gene

  • Serine Palmitoyltransferase Long Chain Base Subunit 2 2 3
  • Serine Palmitoyltransferase, Long Chain Base Subunit 2 3 5
  • Long Chain Base Biosynthesis Protein 2a 3 4
  • Serine-Palmitoyl-CoA Transferase 2 3 4
  • EC 2.3.1.50 4 63
  • LCB 2 3 4
  • SPT 2 3 4
  • LCB2A 3 4
  • LCB2 3 4
  • Serine Palmitoyltransferase, Subunit II 3
  • Long Chain Base Biosynthesis Protein 2 4
  • KIAA0526 4
  • EC 2.3.1 63
  • NSAN1C 3
  • HLCB2a 3
  • HSN1C 3
  • SPT2 3

External Ids for SPTLC2 Gene

Previous GeneCards Identifiers for SPTLC2 Gene

  • GC14M075479
  • GC14M071790
  • GC14M075963
  • GC14M077043
  • GC14M077973
  • GC14M058139

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 Dnmt1-Related Dementia, Deafness, And Sensory Neuropathy. Among its related pathways are Sphingolipid signaling pathway and 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

Regulatory Elements for SPTLC2 Gene

Enhancers for SPTLC2 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SPTLC2 on UCSC Golden Path with GeneCards custom track

Promoters for SPTLC2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SPTLC2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SPTLC2 Gene

Chromosome:
14
Start:
77,505,997 bp from pter
End:
77,616,773 bp from pter
Size:
110,777 bases
Orientation:
Minus strand

Genomic View for SPTLC2 Gene

Genes around SPTLC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTLC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTLC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTLC2 Gene

Proteins for SPTLC2 Gene

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

    Protein Symbol:
    O15270-SPTC2_HUMAN
    Recommended name:
    Serine palmitoyltransferase 2
    Protein Accession:
    O15270
    Secondary Accessions:
    • Q16685

    Protein attributes for SPTLC2 Gene

    Size:
    562 amino acids
    Molecular mass:
    62924 Da
    Cofactor:
    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).
    SequenceCaution:
    • 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

  • Ubiquitination at Lys 161
  • Modification sites at PhosphoSitePlus

Other Protein References for SPTLC2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for SPTLC2 Gene

Suggested Antigen Peptide Sequences for SPTLC2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15270

UniProtKB/Swiss-Prot:

SPTC2_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 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:0016740 transferase activity IEA --
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

Human Phenotype Ontology for SPTLC2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SPTLC2 Gene

MGI Knock Outs for SPTLC2:

Animal Model Products

  • Taconic Biosciences Mouse Models for SPTLC2

miRNA for SPTLC2 Gene

miRTarBase miRNAs that target SPTLC2

No data available for Transcription Factor Targets 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

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

No data available for Gene Ontology (GO) - Cellular Components for SPTLC2 Gene

Pathways & Interactions 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:0008152 metabolic process IEA --
GO:0009058 biosynthetic process IEA --
GO:0030148 sphingolipid biosynthetic process TAS 19416851
GO:0046511 sphinganine biosynthetic process IEA --
GO:0046513 ceramide biosynthetic process IEA --
genes like me logo Genes that share ontologies with SPTLC2: view

No data available for SIGNOR curated interactions for SPTLC2 Gene

Drugs & Compounds for SPTLC2 Gene

(5) Drugs for SPTLC2 Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Serine Approved Nutra Full agonist, Agonist, Target 0
Pyridoxal Phosphate Nutra Target, cofactor 14
Myriocin Pharma 0
Coenzyme A Nutra 0

(6) Additional Compounds for SPTLC2 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
genes like me logo Genes that share compounds with SPTLC2: view

Transcripts 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
SPTLC2
ECgene alternative splicing isoforms for
SPTLC2

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 (x6.1).

Protein differential expression in normal tissues from HIPED for SPTLC2 Gene

This gene is overexpressed in Bone (15.0), Peripheral blood mononuclear cells (13.8), and Breast (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines 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

O15270-SPTC2_HUMAN
Tissue specificity: Widely expressed.
genes like me logo Genes that share expression patterns with SPTLC2: view

Protein tissue co-expression partners for SPTLC2 Gene

Primer Products

Orthologs for SPTLC2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPTLC2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SPTLC2 35
  • 90.73 (n)
  • 95.01 (a)
SPTLC2 36
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SPTLC2 35
  • 92.35 (n)
  • 96.8 (a)
SPTLC2 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sptlc2 35
  • 90.83 (n)
  • 96.43 (a)
Sptlc2 16
Sptlc2 36
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SPTLC2 35
  • 99.58 (n)
  • 100 (a)
SPTLC2 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptlc2 35
  • 89.64 (n)
  • 95.71 (a)
oppossum
(Monodelphis domestica)
Mammalia SPTLC2 36
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SPTLC2 36
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTLC2 35
  • 79.5 (n)
  • 89.21 (a)
SPTLC2 36
  • 86 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPTLC2 36
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc2 35
  • 73.54 (n)
  • 86.77 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2338 35
zebrafish
(Danio rerio)
Actinopterygii Dr.16885 35
sptlc2a 35
  • 72.45 (n)
  • 81.89 (a)
sptlc2a 36
  • 77 (a)
OneToMany
sptlc2b 36
  • 75 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta lace 37
  • 56 (a)
lace 35
  • 59 (n)
  • 57.53 (a)
lace 36
  • 47 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007941 35
  • 59.28 (n)
  • 58.23 (a)
worm
(Caenorhabditis elegans)
Secernentea F43H9.2a 37
  • 55 (a)
F43H9.2b 37
  • 55 (a)
T22G5.5 37
  • 49 (a)
sptl-2 35
  • 57.79 (n)
  • 55.33 (a)
sptl-2 36
  • 45 (a)
ManyToMany
sptl-3 36
  • 45 (a)
ManyToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR127C 35
  • 52.73 (n)
  • 47.95 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D02134g 35
  • 53.42 (n)
  • 47.86 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB2 35
  • 53.31 (n)
  • 48.47 (a)
LCB2 36
  • 43 (a)
OneToMany
LCB2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons LCB2 35
  • 56.59 (n)
  • 53.56 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2016 35
barley
(Hordeum vulgare)
Liliopsida Hv.11007 35
rice
(Oryza sativa)
Liliopsida Os01g0928800 35
  • 56.82 (n)
  • 53.96 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.2702 35
corn
(Zea mays)
Liliopsida Zm.13752 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.835 35
bread mold
(Neurospora crassa)
Ascomycetes NCU00447 35
  • 55.24 (n)
  • 51.75 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lcb2 35
  • 52.82 (n)
  • 50.42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 56 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SPTLC2 (if available)
TreeFam:
Gene Tree for SPTLC2 (if available)

Paralogs for SPTLC2 Gene

Paralogs for SPTLC2 Gene

(1) SIMAP similar genes for SPTLC2 Gene using alignment to 4 proteins:

Pseudogenes.org 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
VAR_064798 Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C)
VAR_064799 Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C)
VAR_064800 Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C)
VAR_069525 Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C)
rs13430 -- 77,506,889(-) TGAAG(C/G)AATAC utr-variant-3-prime

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

Variation tolerance for SPTLC2 Gene

Residual Variation Intolerance Score: 17.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.73; 32.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SPTLC2 Gene

Human Gene Mutation Database (HGMD)
SPTLC2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC2 Gene

Disorders for SPTLC2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SPTLC2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
neuropathy, hereditary sensory and autonomic, type ic
  • hereditary sensory and autonomic neuropathy type ic
dnmt1-related dementia, deafness, and sensory neuropathy
  • hereditary sensoryautonomic neuropathy type 1 with dementiahearing loss
hereditary sensory neuropathy
  • congenital insensitivity to pain
neuropathy
autonomic neuropathy
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPTC2_HUMAN
  • 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}.

Relevant External Links for SPTLC2

Genetic Association Database (GAD)
SPTLC2
Human Genome Epidemiology (HuGE) Navigator
SPTLC2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SPTLC2
genes like me logo Genes that share disorders with SPTLC2: view

No data available for Genatlas for SPTLC2 Gene

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 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 3 23
  3. Is the mammalian serine palmitoyltransferase a high-molecular-mass complex? (PMID: 17331073) Hornemann T. … von Eckardstein A. (Biochem. J. 2007) 3 23
  4. The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. (PMID: 17559874) Yard B.A. … Campopiano D.J. (J. Mol. Biol. 2007) 25 26
  5. 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

Products for SPTLC2 Gene

Sources for SPTLC2 Gene

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