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SPTSSB serine palmitoyltransferase small subunit B [ Homo sapiens (human) ]

Gene ID: 165679, updated on 4-Jan-2025

Summary

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Official Symbol
SPTSSBprovided by HGNC
Official Full Name
serine palmitoyltransferase small subunit Bprovided by HGNC
Primary source
HGNC:HGNC:24045
See related
Ensembl:ENSG00000196542 MIM:610412; AllianceGenome:HGNC:24045
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ADMP; SSSPTB; C3orf57
Summary
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]
Expression
Biased expression in stomach (RPKM 17.1), skin (RPKM 13.9) and 5 other tissues See more
Orthologs
mouse all
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Genomic context

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See SPTSSB in Genome Data Viewer
Location:
3q26.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (161344798..161371517, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (164119563..164146294, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (161062586..161089305, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene 4 Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:161088778-161089332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:161089333-161089887 Neighboring gene uncharacterized LOC107986150 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:161138438-161139086 Neighboring gene long intergenic non-protein coding RNA 2067 Neighboring gene ribosomal protein L23a pseudogene 42

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium. Singh J, et al. Gene, 2005 Mar 28. PMID 15777716
  2. Structural insights into the regulation of human serine palmitoyltransferase complexes. Wang Y, et al. Nat Struct Mol Biol, 2021 Mar. PMID 33558761, Free PMC Article
  3. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. Han G, et al. Proc Natl Acad Sci U S A, 2009 May 19. PMID 19416851, Free PMC Article
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ADMP expression was seen predominantly in the prostate epithelium with weaker expression in the fibroblasts and endothelial cells.
    Title: Molecular cloning and characterization of a novel androgen repressible gene expressed in the prostate epithelium.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

Homology

Clone Names

  • MGC104229

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to serine C-palmitoyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within ceramide biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in endoplasmic reticulum organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within endoplasmic reticulum organization ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within sphingolipid biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in sphingosine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
part_of serine palmitoyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of serine palmitoyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of serine palmitoyltransferase complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
serine palmitoyltransferase small subunit B
Names
androgen down regulated in mouse prostate
likely ortholog of androgen down regulated gene expressed in mouse prostate
small subunit of serine palmitoyltransferase B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001040100.2 → NP_001035189.1  serine palmitoyltransferase small subunit B

    See identical proteins and their annotated locations for NP_001035189.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC112491
    Consensus CDS
    CCDS33887.1
    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
    Related
    ENSP00000480827.1, ENST00000620149.2
    Conserved Domains (1) summary
    pfam11779
    Location:7 → 60
    SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

  2. NM_001320679.2 → NP_001307608.1  serine palmitoyltransferase small subunit B

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC112491
    Consensus CDS
    CCDS33887.1
    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
    Related
    ENSP00000420115.1, ENST00000497137.1
    Conserved Domains (1) summary
    pfam11779
    Location:7 → 60
    SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    161344798..161371517 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453380.2 → XP_024309148.1  serine palmitoyltransferase small subunit B isoform X1

    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
    Conserved Domains (1) summary
    pfam11779
    Location:7 → 60
    SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

  2. XM_024453379.2 → XP_024309147.1  serine palmitoyltransferase small subunit B isoform X1

    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3
    Conserved Domains (1) summary
    pfam11779
    Location:7 → 60
    SPT_ssu-like; Small subunit of serine palmitoyltransferase-like

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    164119563..164146294 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345480.1 → XP_054201455.1  serine palmitoyltransferase small subunit B isoform X1

    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3

  2. XM_054345479.1 → XP_054201454.1  serine palmitoyltransferase small subunit B isoform X1

    UniProtKB/Swiss-Prot
    B2R5D3, D3DNM8, Q0P5S6, Q8NFR3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_145035.2: Suppressed sequence

    Description
    NM_145035.2: This RefSeq was permanently suppressed because it contains the wrong CDS and is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NFR3.1 GenPept UniProtKB/Swiss-Prot:Q8NFR3

Gene LinkOut

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