Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTB is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by... See more...

Aliases for SPTSSB Gene

Aliases for SPTSSB Gene

  • Serine Palmitoyltransferase Small Subunit B 2 3 4 5
  • Small Subunit Of Serine Palmitoyltransferase B 2 3 4
  • Androgen Down Regulated In Mouse Prostate 2 3
  • C3orf57 3 4
  • SSSPTB 3 4
  • ADMP 3 4
  • Likely Ortholog Of Androgen Down Regulated Gene Expressed In Mouse Prostate 3
  • Serine Palmitoyltransferase, Small Subunit B 2
  • Chromosome 3 Open Reading Frame 57 2
  • Protein ADMP 4
  • SsSPTb 4

External Ids for SPTSSB Gene

Previous HGNC Symbols for SPTSSB Gene

  • C3orf57

Previous GeneCards Identifiers for SPTSSB Gene

  • GC03M161063

Summaries for SPTSSB Gene

Entrez Gene Summary for SPTSSB Gene

  • Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTB is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

GeneCards Summary for SPTSSB Gene

SPTSSB (Serine Palmitoyltransferase Small Subunit B) is a Protein Coding gene. Diseases associated with SPTSSB include Hereditary Sensory And Autonomic Neuropathy Type 1 and Phosphoglycerate Dehydrogenase Deficiency. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include serine C-palmitoyltransferase activity. An important paralog of this gene is SPTSSA.

UniProtKB/Swiss-Prot Summary for SPTSSB Gene

  • Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference, complexes with this subunit showing a clear preference for longer acyl-CoAs. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference. May play a role in signal transduction.

Additional gene information for SPTSSB Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPTSSB Gene

Genomics for SPTSSB Gene

GeneHancer (GH) Regulatory Elements for SPTSSB Gene

Promoters and enhancers for SPTSSB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J161370 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 525.9 +1.0 1016 3.4 ZNF217 CTCF TEAD4 ZFX CLOCK ZBTB26 RFX1 CUX1 CHD1 GATAD2B SPTSSB lnc-B3GALNT1-3 PSMC1P7 LINC02067 B3GALNT1 lnc-NMD3-2
GH03J161338 Enhancer 1.2 Ensembl ENCODE dbSUPER 45.7 +33.3 33272 1.6 ZNF217 KDM6A CLOCK TCF7 CUX1 ZBTB25 TEAD1 GATAD2B ZKSCAN8 CTBP1 SPTSSB PSMC1P7 EEF1GP4 L13713-165 lnc-NMD3-2
GH03J161418 Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 33.4 -48.3 -48258 5.2 FOXK2 ZNF217 TCF12 TEAD4 ZFX CTCF KDM6A CLOCK TCF7 FOXA1 NONHSAG036547.2 SPTSSB LINC02067 NMD3
GH03J161220 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 24.5 +150.6 150629 4.2 ZBTB40 ZNF217 EP300 TCF12 POLR2G SP1 PHF8 ZFX REST POLR2A NMD3 ENSG00000271052 lnc-B3GALNT1-2 SPTSSB B3GALNT1 PSMC1P7 IFT80 EEF1GP4 piR-56883-117
GH03J161332 Enhancer 1.1 Ensembl ENCODE dbSUPER 45.5 +39.2 39237 2.2 CUX1 FOXA2 CEBPB SAP130 SPI1 ZGPAT FOSL2 BCL6 HOMEZ THAP11 SPTSSB PSMC1P7 L13713-165 lnc-NMD3-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTSSB on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPTSSB

Genomic Locations for SPTSSB Gene

Genomic Locations for SPTSSB Gene
chr3:161,344,792-161,372,938
(GRCh38/hg38)
Size:
28,147 bases
Orientation:
Minus strand
chr3:161,062,580-161,090,668
(GRCh37/hg19)
Size:
28,089 bases
Orientation:
Minus strand

Genomic View for SPTSSB Gene

Genes around SPTSSB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SPTSSB Gene

Proteins for SPTSSB Gene

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

    Protein Symbol:
    Q8NFR3-SPTSB_HUMAN
    Recommended name:
    Serine palmitoyltransferase small subunit B
    Protein Accession:
    Q8NFR3
    Secondary Accessions:
    • B2R5D3
    • D3DNM8
    • Q0P5S6

    Protein attributes for SPTSSB Gene

    Size:
    76 amino acids
    Molecular mass:
    9198 Da
    Quaternary structure:
    • Interacts with SPTLC1; the interaction is direct. Component of the serine palmitoyltransferase (SPT) complex, composed of SPTLC1, either SPTLC2 or SPTLC3, and either SPTSSA or SPTSSB.

neXtProt entry for SPTSSB Gene

Post-translational modifications for SPTSSB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPTSSB Gene

Domains & Families for SPTSSB Gene

Gene Families for SPTSSB Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SPTSSB Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPTSSB Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ41354 fis, clone BRAWH2014876 (Q6ZWB5_HUMAN)
  • Protein ADMP (SSPTB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NFR3

UniProtKB/Swiss-Prot:

SPTSB_HUMAN :
  • Belongs to the SPTSS family. SPTSSB subfamily.
Family:
  • Belongs to the SPTSS family. SPTSSB subfamily.
genes like me logo Genes that share domains with SPTSSB: view

Function for SPTSSB Gene

Molecular function for SPTSSB Gene

UniProtKB/Swiss-Prot Function:
Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference, complexes with this subunit showing a clear preference for longer acyl-CoAs. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference. May play a role in signal transduction.
UniProtKB/Swiss-Prot Induction:
Expression is suppressed by androgens in the androgen-sensitive LNCaP cell line.

Phenotypes From GWAS Catalog for SPTSSB Gene

Gene Ontology (GO) - Molecular Function for SPTSSB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004758 contributes_to serine C-palmitoyltransferase activity IDA 19416851
GO:0005515 protein binding IPI 19416851
genes like me logo Genes that share ontologies with SPTSSB: view
genes like me logo Genes that share phenotypes with SPTSSB: view

Animal Models for SPTSSB Gene

MGI Knock Outs for SPTSSB:
  • Sptssb Sptssb<tm1b(KOMP)Mbp>

Animal Model Products

CRISPR Products

miRNA for SPTSSB Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTSSB

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPTSSB Gene

Localization for SPTSSB Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTSSB Gene

Endoplasmic reticulum membrane; Multi-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 SPTSSB gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 2
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPTSSB 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,IBA 19416851
genes like me logo Genes that share ontologies with SPTSSB: view

Pathways & Interactions for SPTSSB Gene

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

Pathways by source for SPTSSB Gene

UniProtKB/Swiss-Prot Q8NFR3-SPTSB_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SPTSSB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0007029 endoplasmic reticulum organization ISS,IBA --
GO:0030148 sphingolipid biosynthetic process TAS,ISS 19416851
GO:0046513 ceramide biosynthetic process ISS --
genes like me logo Genes that share ontologies with SPTSSB: view

No data available for SIGNOR curated interactions for SPTSSB Gene

Drugs & Compounds for SPTSSB Gene

No Compound Related Data Available

Transcripts for SPTSSB Gene

mRNA/cDNA for SPTSSB Gene

3 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPTSSB

Clone Products

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

No ASD Table

Relevant External Links for SPTSSB Gene

GeneLoc Exon Structure for
SPTSSB

Expression for SPTSSB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x7.4), Skin - Sun Exposed (Lower leg) (x7.2), and Bladder (x6.9).

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPTSSB

SOURCE GeneReport for Unigene cluster for SPTSSB Gene:

Hs.369104

mRNA Expression by UniProt/SwissProt for SPTSSB Gene:

Q8NFR3-SPTSB_HUMAN
Tissue specificity: Expression is seen predominantly in the prostate epithelium with weaker expression in the fibroblasts and endothelial cells.

Evidence on tissue expression from TISSUES for SPTSSB Gene

  • Nervous system(4.4)
  • Lung(4)
genes like me logo Genes that share expression patterns with SPTSSB: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTSSB Gene

Orthologs for SPTSSB Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPTSSB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPTSSB 31 30
  • 100 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPTSSB 31 30
  • 90.79 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPTSSB 31 30
  • 90.35 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sptssb 30
  • 88.16 (n)
mouse
(Mus musculus)
Mammalia Sptssb 17 31 30
  • 85.53 (n)
oppossum
(Monodelphis domestica)
Mammalia SPTSSB 31
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPTSSB 31 30
  • 71.11 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPTSSB 31
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sptssb 30
  • 67.11 (n)
zebrafish
(Danio rerio)
Actinopterygii sptssb 31 30
  • 63.29 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3848 31
  • 15 (a)
OneToMany
Species where no ortholog for SPTSSB 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SPTSSB Gene

ENSEMBL:
Gene Tree for SPTSSB (if available)
TreeFam:
Gene Tree for SPTSSB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTSSB: view image

Paralogs for SPTSSB Gene

Paralogs for SPTSSB Gene

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

  • SPTSB_HUMAN
genes like me logo Genes that share paralogs with SPTSSB: view

Variants for SPTSSB Gene

Additional dbSNP identifiers (rs#s) for SPTSSB Gene

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

Variant ID Type Subtype PubMed ID
esv2726119 CNV deletion 23290073
esv3598407 CNV gain 21293372
nsv4091 CNV deletion 18451855
nsv592128 CNV loss 21841781
nsv829770 CNV gain 17160897
nsv829772 CNV gain+loss 17160897

Variation tolerance for SPTSSB Gene

Residual Variation Intolerance Score: 58.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.10; 2.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTSSB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTSSB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPTSSB Gene

Disorders for SPTSSB Gene

MalaCards: The human disease database

(7) MalaCards diseases for SPTSSB Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SPTSSB

genes like me logo Genes that share disorders with SPTSSB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPTSSB Gene

Publications for SPTSSB Gene

  1. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. (PMID: 19416851) Han G … Dunn TM (Proceedings of the National Academy of Sciences of the United States of America 2009) 2 3 4 54
  2. Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium. (PMID: 15777716) Singh J … Dong Q (Gene 2005) 2 3 4 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 54

Products for SPTSSB Gene

Sources for SPTSSB Gene