Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTA 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 SPTSSA Gene

Aliases for SPTSSA Gene

  • Serine Palmitoyltransferase Small Subunit A 2 3 4 5
  • Small Subunit Of Serine Palmitoyltransferase A 2 3 4
  • C14orf147 3 4
  • SSSPTA 3 4
  • SsSPTa 2 4
  • Serine Palmitoyltransferase, Small Subunit A 2
  • Chromosome 14 Open Reading Frame 147 2
  • SPTSSA 5

External Ids for SPTSSA Gene

Previous HGNC Symbols for SPTSSA Gene

  • C14orf147

Previous GeneCards Identifiers for SPTSSA Gene

  • GC14M034902

Summaries for SPTSSA Gene

Entrez Gene Summary for SPTSSA Gene

  • Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTA 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 SPTSSA Gene

SPTSSA (Serine Palmitoyltransferase Small Subunit A) is a Protein Coding gene. Diseases associated with SPTSSA include Nephrotic Syndrome, Type 14 and Hereditary Sensory And Autonomic Neuropathy Type 1. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include serine C-palmitoyltransferase activity.

UniProtKB/Swiss-Prot Summary for SPTSSA Gene

  • Stimulates the activity of serine palmitoyltransferase (SPT). 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA (PubMed:19416851). Plays a role in MBOAT7 location to mitochondria-associated membranes (MAMs), may me involved in fatty acid remodeling phosphatidylinositol (PI) (PubMed:23510452).

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

Genomics for SPTSSA Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPTSSA 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
GH14J034460 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.5 539 3.8 ZNF207 NCOR1 MYC IKZF1 SSRP1 ZNF580 ATF2 POLR2A CEBPA BRCA1 EGLN3 SPTSSA lnc-EGLN3-1 RPS19P3 EAPP HSALNG0100509 HSALNG0100510
GH14J034434 Promoter 0.3 EPDnew 261.4 +27.5 27501 0.1 SPTSSA HSALNG0100508 piR-38717-003 lnc-EGLN3-1 EGLN3
GH14J034367 Enhancer 1.3 FANTOM5 Ensembl ENCODE 19.8 +90.7 90740 9 CEBPA CEBPB FOXA1 KLF11 HOMEZ MAX ZNF217 EP300 NONO THAP11 SPTSSA RPS19P3 EAPP HSALNG0100506 HSALNG0100504 EGLN3 lnc-EGLN3-1
GH14J034379 Enhancer 0.8 Ensembl ENCODE 16.9 +82.2 82186 2.1 CEBPA CEBPB SMAD4 TBP TCF7L2 PRDM6 GATA3 HMG20A GLIS1 IKZF5 SPTSSA HSALNG0100506 piR-50308-165 lnc-EGLN3-1 EGLN3
GH14J034362 Enhancer 0.8 Ensembl ENCODE 16.5 +98.9 98939 5 CEBPB CTCF ZNF217 FOXA2 KDM6A CTBP1 RAD21 CUX1 ZSCAN9 PRDM10 HSALNG0100504 SPTSSA EAPP HSALNG0100506 EGLN3 lnc-EGLN3-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPTSSA on the GeneHancer Hub at the UCSC Golden Path

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

Genomic Locations for SPTSSA Gene

Latest Assembly
chr14:34,432,788-34,462,240
(GRCh38/hg38)
Size:
29,453 bases
Orientation:
Minus strand

Previous Assembly
chr14:34,901,994-34,931,446
(GRCh37/hg19 by Entrez Gene)
Size:
29,453 bases
Orientation:
Minus strand

chr14:34,901,995-34,931,562
(GRCh37/hg19 by Ensembl)
Size:
29,568 bases
Orientation:
Minus strand

Genomic View for SPTSSA Gene

Genes around SPTSSA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SPTSSA Gene

Proteins for SPTSSA Gene

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

    Protein Symbol:
    Q969W0-SPTSA_HUMAN
    Recommended name:
    Serine palmitoyltransferase small subunit A
    Protein Accession:
    Q969W0
    Secondary Accessions:
    • B2RD54
    • D3DS93
    • Q8WTZ7

    Protein attributes for SPTSSA Gene

    Size:
    71 amino acids
    Molecular mass:
    8466 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 (PubMed:19416851). Interacts with MBOAT7; the interaction facilitates MBOAT7 location to mitochondria-associated membranes (MAMs) (PubMed:23510452).
    SequenceCaution:
    • Sequence=AAH16805.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH16808.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH21701.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH68480.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAG37801.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for SPTSSA Gene

Post-translational modifications for SPTSSA Gene

No Post-translational modifications

Other Protein References for SPTSSA Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPTSSA Gene

Domains & Families for SPTSSA Gene

Gene Families for SPTSSA Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SPTSSA Gene

Suggested Antigen Peptide Sequences for SPTSSA Gene

GenScript: Design optimal peptide antigens:
  • Small subunit of serine palmitoyltransferase A (SSPTA_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q969W0

UniProtKB/Swiss-Prot:

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

Function for SPTSSA Gene

Molecular function for SPTSSA Gene

UniProtKB/Swiss-Prot Function:
Stimulates the activity of serine palmitoyltransferase (SPT). 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA (PubMed:19416851). Plays a role in MBOAT7 location to mitochondria-associated membranes (MAMs), may me involved in fatty acid remodeling phosphatidylinositol (PI) (PubMed:23510452).

Phenotypes From GWAS Catalog for SPTSSA Gene

Gene Ontology (GO) - Molecular Function for SPTSSA Gene

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

Animal Models for SPTSSA Gene

MGI Knock Outs for SPTSSA:
  • Sptssa Sptssa<tm1b(KOMP)Wtsi>

Inhibitory RNAs for research

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

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

Localization for SPTSSA Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPTSSA 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 SPTSSA gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 3
mitochondrion 2
nucleus 2
cytosol 2
plasma membrane 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SPTSSA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IDA 23510452
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0017059 serine C-palmitoyltransferase complex IBA,IDA 19416851
genes like me logo Genes that share ontologies with SPTSSA: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPTSSA Gene

Pathways & Interactions for SPTSSA Gene

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

Pathways by source for SPTSSA Gene

UniProtKB/Swiss-Prot Q969W0-SPTSA_HUMAN

  • Pathway: Lipid metabolism; sphingolipid metabolism.

Gene Ontology (GO) - Biological Process for SPTSSA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006665 sphingolipid metabolic process IEA --
GO:0008104 protein localization IDA 23510452
GO:0030148 sphingolipid biosynthetic process TAS 19416851
GO:0046513 ceramide biosynthetic process IDA 25691431
genes like me logo Genes that share ontologies with SPTSSA: view

No data available for SIGNOR curated interactions for SPTSSA Gene

Drugs & Compounds for SPTSSA Gene

No Compound Related Data Available

Transcripts for SPTSSA Gene

mRNA/cDNA for SPTSSA Gene

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

Inhibitory RNAs for research

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

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

No ASD Table

Relevant External Links for SPTSSA Gene

GeneLoc Exon Structure for
SPTSSA

Expression for SPTSSA Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPTSSA Gene

This gene is overexpressed in Monocytes (69.0).

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



Protein tissue co-expression partners for SPTSSA Gene

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

SOURCE GeneReport for Unigene cluster for SPTSSA Gene:

Hs.740577

Evidence on tissue expression from TISSUES for SPTSSA Gene

  • Nervous system(4.4)
  • Kidney(4.3)
  • Bone marrow(4.1)
genes like me logo Genes that share expression patterns with SPTSSA: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPTSSA Gene

Orthologs for SPTSSA Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPTSSA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPTSSA 29 30
  • 99.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SPTSSA 30
  • 97 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SPTSSA 29 30
  • 95.1 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sptssa 29 16 30
  • 91.08 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SPTSSA 30
  • 91 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sptssa 29
  • 90.61 (n)
Chicken
(Gallus gallus)
Aves SPTSSA 29 30
  • 87.75 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SPTSSA 30
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sptssa 29
  • 80.6 (n)
Str.8281 29
Zebrafish
(Danio rerio)
Actinopterygii sptssa 29 30
  • 73.53 (n)
OneToOne
wufb60h11 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8612 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3848 30
  • 18 (a)
OneToMany
Species where no ortholog for SPTSSA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 SPTSSA Gene

ENSEMBL:
Gene Tree for SPTSSA (if available)
TreeFam:
Gene Tree for SPTSSA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPTSSA: view image
Alliance of Genome Resources:
Additional Orthologs for SPTSSA

Paralogs for SPTSSA Gene

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

  • SPTSA_HUMAN

Pseudogenes.org Pseudogenes for SPTSSA Gene

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

No data available for Paralogs for SPTSSA Gene

Variants for SPTSSA Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPTSSA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv3608n54 CNV gain 21841781
nsv1048369 CNV gain 25217958
nsv1050218 CNV gain 25217958
nsv528989 CNV gain 19592680

Variation tolerance for SPTSSA Gene

Residual Variation Intolerance Score: 56.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.15; 3.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPTSSA Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPTSSA
Leiden Open Variation Database (LOVD)
SPTSSA

SNP Genotyping and Copy Number Assays for research

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 SPTSSA Gene

Disorders for SPTSSA Gene

MalaCards: The human disease database

(7) MalaCards diseases for SPTSSA Gene - From: COP

Disorder Aliases PubMed IDs
nephrotic syndrome, type 14
  • nphs14
hereditary sensory and autonomic neuropathy type 1
  • hereditary sensory and autonomic neuropathy type i
neuropathy, hereditary sensory and autonomic, type ia
  • hsan1a
phosphoglycerate dehydrogenase deficiency
  • phgdhd
alveoli adenoma
  • adenoma of alveoli
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SPTSSA

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

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

Publications for SPTSSA 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
  2. Identification of small subunit of serine palmitoyltransferase a as a lysophosphatidylinositol acyltransferase 1-interacting protein. (PMID: 23510452) Hirata Y … Arai H (Genes to cells : devoted to molecular & cellular mechanisms 2013) 3 4
  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
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for SPTSSA Gene

Sources for SPTSSA Gene