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Aliases for SPTLC3 Gene

Aliases for SPTLC3 Gene

  • Serine Palmitoyltransferase Long Chain Base Subunit 3 2 3 5
  • Serine Palmitoyltransferase, Long Chain Base Subunit 2-Like (Aminotransferase 2) 2 3
  • Long Chain Base Biosynthesis Protein 2b 3 4
  • Long Chain Base Biosynthesis Protein 3 3 4
  • Serine-Palmitoyl-CoA Transferase 3 3 4
  • EC 2.3.1.50 4 61
  • C20orf38 3 4
  • SPTLC2L 3 4
  • LCB 3 3 4
  • SPT 3 3 4
  • LCB2B 3 4
  • Chromosome 20 Open Reading Frame 38 2
  • Serine Palmitoyltransferase 3 3
  • DJ718P11.1 3
  • DJ718P11 3
  • EC 2.3.1 61
  • HLCB2b 3
  • LCB3 3
  • SPT3 3

External Ids for SPTLC3 Gene

Previous HGNC Symbols for SPTLC3 Gene

  • C20orf38
  • SPTLC2L

Previous GeneCards Identifiers for SPTLC3 Gene

  • GC20P012938

Summaries for SPTLC3 Gene

Entrez Gene Summary for SPTLC3 Gene

  • This gene encodes a subunit of the serine palmitoyltransferase complex which catalyzes the rate-limiting step in sphingolipid biosynthesis. This subunit metabolizes lauroyl- and myristoyl-CoA and generates C14 and C16-sphingoid bases. [provided by RefSeq, Mar 2017]

GeneCards Summary for SPTLC3 Gene

SPTLC3 (Serine Palmitoyltransferase Long Chain Base Subunit 3) is a Protein Coding gene. Among its related pathways are Sphingolipid metabolism and Sphingolipid signaling pathway. GO annotations related to this gene include pyridoxal phosphate binding and transaminase activity. An important paralog of this gene is SPTLC2.

UniProtKB/Swiss-Prot for SPTLC3 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPTLC3 Gene

Genomics for SPTLC3 Gene

Regulatory Elements for SPTLC3 Gene

Enhancers for SPTLC3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20G013054 0.9 FANTOM5 ENCODE 30.9 +46.4 46370 1.8 CEBPA HLF NBN CEBPB CEBPG EZH2 SPTLC3 LOC100420611
GH20G012976 1.2 ENCODE dbSUPER 21.6 -31.5 -31526 1.8 ELF3 HNRNPUL1 PKNOX1 FOXA2 MLX ZFP64 RAD21 RARA GATA4 CREM SPTLC3 ISM1 LINC01722
GH20G012979 1.1 ENCODE dbSUPER 22.7 -29.8 -29758 0.4 ELF3 FOXA2 ATF1 ARID4B DMAP1 RAD21 RARA GATA4 CREM MIXL1 SPTLC3 LINC01722
GH20G013027 1.2 Ensembl ENCODE 16.7 +20.5 20543 3.5 ATF1 ZFP64 SIN3A ARID4B FEZF1 DMAP1 ZNF48 YY1 FOS SP5 SPTLC3 LOC100420611
GH20G013089 0.9 ENCODE 16.2 +81.0 81008 1.5 HNRNPUL1 FOXA2 ATF1 MLX ARID4B ZNF48 SLC30A9 NFYC PPARG KAT8 SPTLC3 LOC100420611 GC20P013112
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SPTLC3 on UCSC Golden Path with GeneCards custom track

Promoters for SPTLC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000134804 421 1201 ELF3 ATF1 ZFP64 ARID4B BMI1 ZNF48 RAD21 YY1 RELB IKZF2

Genomic Location for SPTLC3 Gene

Chromosome:
20
Start:
13,008,979 bp from pter
End:
13,170,944 bp from pter
Size:
161,966 bases
Orientation:
Plus strand

Genomic View for SPTLC3 Gene

Genes around SPTLC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPTLC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPTLC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPTLC3 Gene

Proteins for SPTLC3 Gene

  • Protein details for SPTLC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUV7-SPTC3_HUMAN
    Recommended name:
    Serine palmitoyltransferase 3
    Protein Accession:
    Q9NUV7
    Secondary Accessions:
    • A2A2I4
    • B9EK64
    • Q05DQ8
    • Q5T1U4
    • Q9H1L1
    • Q9H1Z0

    Protein attributes for SPTLC3 Gene

    Size:
    552 amino acids
    Molecular mass:
    62049 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=AAH05205.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Alternative splice isoforms for SPTLC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPTLC3 Gene

Selected DME Specific Peptides for SPTLC3 Gene

Q9NUV7:
  • RNLYMRIRD
  • VVVVGFPAT
  • MGTFTKSF
  • GMGFATNSMNIPALVGKGCLILSDELNH
  • LFGYLRDF
  • LYIDEAH
  • YGQPRTRR
  • VINMGSYN
  • HSHSAVYA
  • SLVLGARLSGATIRIFKHNN
  • ALKKKYKAYLY
  • YSMEGSIV
  • LYQDFENFY

Post-translational modifications for SPTLC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPTLC3 Gene

Domains & Families for SPTLC3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NUV7

UniProtKB/Swiss-Prot:

SPTC3_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 SPTLC3: view

No data available for Gene Families for SPTLC3 Gene

Function for SPTLC3 Gene

Molecular function for SPTLC3 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference.

Enzyme Numbers (IUBMB) for SPTLC3 Gene

Gene Ontology (GO) - Molecular Function for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004758 serine C-palmitoyltransferase activity TAS --
GO:0008483 transaminase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016746 transferase activity, transferring acyl groups IEA --
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with SPTLC3: view

Phenotypes for SPTLC3 Gene

genes like me logo Genes that share phenotypes with SPTLC3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPTLC3 Gene

Localization for SPTLC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTLC3 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPTLC3 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 3
nucleus 2
cytosol 2

Gene Ontology (GO) - Cellular Components for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IDA 17331073
genes like me logo Genes that share ontologies with SPTLC3: view

Pathways & Interactions for SPTLC3 Gene

genes like me logo Genes that share pathways with SPTLC3: view

Pathways by source for SPTLC3 Gene

UniProtKB/Swiss-Prot Q9NUV7-SPTC3_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0008152 metabolic process IEA --
GO:0009058 biosynthetic process IEA --
GO:0030148 sphingolipid biosynthetic process TAS 19416851
genes like me logo Genes that share ontologies with SPTLC3: view

No data available for SIGNOR curated interactions for SPTLC3 Gene

Drugs & Compounds for SPTLC3 Gene

(5) Drugs for SPTLC3 Gene - From: DrugBank, DGIdb, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Carbon dioxide Approved, Vet_approved Pharma 0
L-Serine Approved Nutra Full agonist, Agonist Weak endogenous glycine receptor agonist 0
Pyridoxal Phosphate Nutra Target, cofactor 15
Myriocin Pharma 0
Coenzyme A Nutra 0

(2) Additional Compounds for SPTLC3 Gene - From: HMDB

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
hexadecanoyl-CoA
genes like me logo Genes that share compounds with SPTLC3: view

Transcripts for SPTLC3 Gene

Unigene Clusters for SPTLC3 Gene

Serine palmitoyltransferase, long chain base subunit 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPTLC3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4
SP1: -
SP2: -
SP3:

Relevant External Links for SPTLC3 Gene

GeneLoc Exon Structure for
SPTLC3
ECgene alternative splicing isoforms for
SPTLC3

Expression for SPTLC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPTLC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPTLC3 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x7.1) and Skin - Not Sun Exposed (Suprapubic) (x6.6).

Protein differential expression in normal tissues from HIPED for SPTLC3 Gene

This gene is overexpressed in Placenta (66.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SPTLC3 Gene



Protein tissue co-expression partners for SPTLC3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SPTLC3 Gene:

SPTLC3

SOURCE GeneReport for Unigene cluster for SPTLC3 Gene:

Hs.425023

mRNA Expression by UniProt/SwissProt for SPTLC3 Gene:

Q9NUV7-SPTC3_HUMAN
Tissue specificity: Expressed in most tissues, except peripheral blood cells and bone marrow, with highest levels in heart, kidney, liver, uterus and skin.

Evidence on tissue expression from TISSUES for SPTLC3 Gene

  • Nervous system(4.2)
  • Liver(2.1)
genes like me logo Genes that share expression patterns with SPTLC3: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTLC3 Gene

Orthologs for SPTLC3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SPTLC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPTLC3 35 34
  • 99.46 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPTLC3 35 34
  • 89.01 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPTLC3 35 34
  • 85.61 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SPTLC3 35
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SPTLC3 35
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptlc3 34
  • 77.37 (n)
mouse
(Mus musculus)
Mammalia Sptlc3 35 16 34
  • 76.53 (n)
OneToOne
chicken
(Gallus gallus)
Aves SPTLC3 34 35
  • 74 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 82 (a)
OneToMany
-- 35
  • 68 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc3 34
  • 71.61 (n)
zebrafish
(Danio rerio)
Actinopterygii sptlc3 35 34
  • 67.41 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta lace 35
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sptl-2 35
  • 44 (a)
ManyToMany
sptl-3 35
  • 42 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB2 35
  • 40 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToMany
Species where no ortholog for SPTLC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SPTLC3 Gene

ENSEMBL:
Gene Tree for SPTLC3 (if available)
TreeFam:
Gene Tree for SPTLC3 (if available)

Paralogs for SPTLC3 Gene

Paralogs for SPTLC3 Gene

(2) SIMAP similar genes for SPTLC3 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with SPTLC3: view

Variants for SPTLC3 Gene

Sequence variations from dbSNP and Humsavar for SPTLC3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs755919784 Likely pathogenic 13,072,400(+) ATAAC(C/T)GGACG nc-transcript-variant, reference, missense
rs1000004749 -- 13,156,326(+) TGAAC(C/G)AACCC intron-variant
rs1000019462 -- 13,119,602(+) GGGTC(A/G)CATTG intron-variant
rs1000026967 -- 13,129,482(+) TTAAG(C/G)AAAAA intron-variant
rs1000030069 -- 13,045,929(+) CTCAG(A/G)AATGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SPTLC3 Gene

Variant ID Type Subtype PubMed ID
dgv4247n100 CNV gain 25217958
esv2017186 CNV deletion 18987734
esv2722196 CNV deletion 23290073
esv2722197 CNV deletion 23290073
esv2722198 CNV deletion 23290073
esv3645279 CNV loss 21293372
esv3893288 CNV gain 25118596
nsv1073045 CNV deletion 25765185
nsv1123455 CNV deletion 24896259
nsv518184 CNV gain 19592680
nsv833923 CNV gain+loss 17160897
nsv833924 CNV gain 17160897

Variation tolerance for SPTLC3 Gene

Residual Variation Intolerance Score: 9.58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.16; 51.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SPTLC3 Gene

Human Gene Mutation Database (HGMD)
SPTLC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTLC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPTLC3 Gene

Disorders for SPTLC3 Gene

Relevant External Links for SPTLC3

Genetic Association Database (GAD)
SPTLC3
Human Genome Epidemiology (HuGE) Navigator
SPTLC3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SPTLC3

No disorders were found for SPTLC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPTLC3 Gene

Publications for SPTLC3 Gene

  1. Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase. (PMID: 17023427) Hornemann T. … von Eckardstein A. (J. Biol. Chem. 2006) 2 3 4 64
  2. Genome-wide association study of personality traits in bipolar patients. (PMID: 21368711) Alliey-Rodriguez N. … Gershon E.S. (Psychiatr. Genet. 2011) 3 46 64
  3. A genome-wide perspective of genetic variation in human metabolism. (PMID: 20037589) Illig T. … Suhre K. (Nat. Genet. 2010) 3 46 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64

Products for SPTLC3 Gene

Sources for SPTLC3 Gene

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