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Aliases for SPTLC3 Gene

Aliases for SPTLC3 Gene

  • Serine Palmitoyltransferase, Long Chain Base Subunit 3 2 3
  • 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 63
  • C20orf38 3 4
  • SPTLC2L 3 4
  • LCB 3 3 4
  • SPT 3 3 4
  • LCB2B 3 4
  • Chromosome 20 Open Reading Frame 38 2
  • DJ718P11.1 3
  • DJ718P11 3
  • EC 2.3.1 63
  • HLCB2b 3
  • SPT3 3
  • LCB3 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

  • The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

GeneCards Summary for SPTLC3 Gene

SPTLC3 (Serine Palmitoyltransferase, Long Chain Base Subunit 3) is a Protein Coding gene. Among its related pathways are Metabolism and Sphingolipid metabolism. 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 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

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
GeneLoc Logo Gene 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

Proteomics data for SPTLC3 Gene at MOPED

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:0003824 catalytic activity --
GO:0004758 serine C-palmitoyltransferase activity IDA 19416851
GO:0008483 transaminase activity --
GO:0016740 transferase activity --
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with SPTLC3: view

Phenotypes for SPTLC3 Gene

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

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SPTLC3

In Situ Assay Products

Flow Cytometry Products

No data available for 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
Jensen Localization Image for SPTLC3 Gene COMPARTMENTS Subcellular localization image for SPTLC3 gene
Compartment Confidence
endoplasmic reticulum 5

Gene Ontology (GO) - Cellular Components for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane TAS --
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

Interacting Proteins for SPTLC3 Gene

Gene Ontology (GO) - Biological Process for SPTLC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006665 sphingolipid metabolic process TAS --
GO:0008152 metabolic process --
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 SPTLC3: view

No data available for SIGNOR curated interactions for SPTLC3 Gene

Drugs & Compounds for SPTLC3 Gene

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

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

(3) 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
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
124-38-9
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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SPTLC3

Flow Cytometry 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 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, MOPED, and MaxQB for SPTLC3 Gene



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.
genes like me logo Genes that share expression patterns with SPTLC3: view

Protein tissue co-expression partners for SPTLC3 Gene

- Elite partner

Primer Products

In Situ Assay Products

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
cow
(Bos Taurus)
Mammalia SPTLC3 35
  • 85.61 (n)
  • 86.16 (a)
SPTLC3 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SPTLC3 35
  • 89.01 (n)
  • 90.04 (a)
SPTLC3 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sptlc3 35
  • 76.53 (n)
  • 70.42 (a)
Sptlc3 16
Sptlc3 36
  • 69 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SPTLC3 35
  • 99.46 (n)
  • 99.64 (a)
SPTLC3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptlc3 35
  • 77.37 (n)
  • 71.32 (a)
oppossum
(Monodelphis domestica)
Mammalia SPTLC3 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SPTLC3 36
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTLC3 35
  • 74 (n)
  • 76.18 (a)
SPTLC3 36
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 68 (a)
OneToMany
-- 36
  • 82 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia sptlc3 35
  • 71.61 (n)
  • 76.44 (a)
zebrafish
(Danio rerio)
Actinopterygii sptlc3 35
  • 67.41 (n)
  • 72.04 (a)
sptlc3 36
  • 69 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta lace 36
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea sptl-2 36
  • 44 (a)
ManyToMany
sptl-3 36
  • 42 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LCB2 36
  • 40 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 52 (a)
OneToMany
Species with no ortholog for SPTLC3:
  • 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 MAF
rs85682 -- 13,067,969(+) GATAT(A/G)CTCTT intron-variant
rs171500 -- 13,089,841(+) tcatc(A/G)tacta intron-variant
rs171501 -- 13,084,374(-) CAGCT(C/G)TTAGC intron-variant
rs173399 -- 13,089,596(+) gcctg(C/T)gcaac intron-variant
rs184856 -- 13,007,292(-) AGGTA(C/T)ATATA upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
nsv912684 CNV Loss 21882294
nsv518184 CNV Gain 19592680
nsv833923 CNV Gain+Loss 17160897
nsv833924 CNV Gain 17160897
esv2017186 CNV Deletion 18987734
esv2722196 CNV Deletion 23290073
esv2722197 CNV Deletion 23290073
esv2722198 CNV Deletion 23290073
nsv912685 CNV Gain 21882294

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

HapMap Linkage Disequilibrium report
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
genes like me logo Genes that share disorders with SPTLC3: view

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 67
  2. Genetic loci associated with circulating levels of very long-chain saturated fatty acids. (PMID: 25378659) Lemaitre R.N. … Friedlander Y. (J. Lipid Res. 2015) 67
  3. An atlas of genetic influences on human blood metabolites. (PMID: 24816252) Shin S.Y. … Soranzo N. (Nat. Genet. 2014) 67
  4. Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study. (PMID: 23192594) Velez Edwards D.R. … Edwards T.L. (Hum. Genet. 2013) 67
  5. Discovery and refinement of loci associated with lipid levels. (PMID: 24097068) . … Abecasis G.R. (Nat. Genet. 2013) 67

Products for SPTLC3 Gene

Sources for SPTLC3 Gene

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