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SPTLC3 serine palmitoyltransferase long chain base subunit 3 [ Homo sapiens (human) ]

Gene ID: 55304, updated on 25-Nov-2021

Summary

Official Symbol
SPTLC3provided by HGNC
Official Full Name
serine palmitoyltransferase long chain base subunit 3provided by HGNC
Primary source
HGNC:HGNC:16253
See related
Ensembl:ENSG00000172296 MIM:611120
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LCB3; SPT3; LCB 3; LCB2B; SPT 3; hLCB2b; SPTLC2L; C20orf38; dJ718P11; dJ718P11.1
Summary
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]
Expression
Broad expression in placenta (RPKM 7.5), thyroid (RPKM 7.0) and 22 other tissues See more
Orthologs
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Genomic context

See SPTLC3 in Genome Data Viewer
Location:
20p12.1
Exon count:
15
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (13008972..13169103)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (12989620..13149750)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1722 Neighboring gene uncharacterized LOC102606466 Neighboring gene uncharacterized LOC105372535 Neighboring gene long intergenic non-protein coding RNA 1723 Neighboring gene centrosomal AT-AC splicing factor pseudogene Neighboring gene taspase 1 Neighboring gene uncharacterized LOC105372539 Neighboring gene Sharpr-MPRA regulatory region 1935 Neighboring gene ISM1 antisense RNA 1 Neighboring gene isthmin 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
An atlas of genetic influences on human blood metabolites.
GeneReviews: Not available
Discovery and refinement of loci associated with lipid levels.
GeneReviews: Not available
Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study.
GeneReviews: Not available
Genetic determinants of circulating sphingolipid concentrations in European populations.
GeneReviews: Not available
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
GeneReviews: Not available
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
GeneReviews: Not available
Genome-wide association study of personality traits in bipolar patients.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11112, FLJ90790

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
 
enables serine C-palmitoyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
part_of serine C-palmitoyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of serine C-palmitoyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of serine C-palmitoyltransferase complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
serine palmitoyltransferase 3
Names
long chain base biosynthesis protein 2b
long chain base biosynthesis protein 3
serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)
serine-palmitoyl-CoA transferase 3
NP_001336874.1
NP_060797.2
XP_011527581.1
XP_011527582.1
XP_016883411.1

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.

Genomic

  1. NG_053155.1 RefSeqGene

    Range
    4976..162786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001349945.2NP_001336874.1  serine palmitoyltransferase 3

    Status: REVIEWED

    Source sequence(s)
    AL050320, AL109983, AL133331, AL445589
    Consensus CDS
    CCDS13115.2
    Conserved Domains (1) summary
    PLN02483
    Location:57549
    PLN02483; serine palmitoyltransferase
  2. NM_018327.4NP_060797.2  serine palmitoyltransferase 3

    See identical proteins and their annotated locations for NP_060797.2

    Status: REVIEWED

    Source sequence(s)
    AL050320, AL109983, AL133331, AL445589
    Consensus CDS
    CCDS13115.2
    UniProtKB/Swiss-Prot
    Q9NUV7
    Related
    ENSP00000381968.2, ENST00000399002.7
    Conserved Domains (1) summary
    PLN02483
    Location:57549
    PLN02483; serine palmitoyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    13008972..13169103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529279.1XP_011527581.1  serine palmitoyltransferase 3 isoform X1

    Conserved Domains (2) summary
    PLN02483
    Location:57514
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:109517
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
  2. XM_017027922.1XP_016883411.1  serine palmitoyltransferase 3 isoform X3

  3. XM_011529280.2XP_011527582.1  serine palmitoyltransferase 3 isoform X2

    Conserved Domains (2) summary
    PLN02483
    Location:11358
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:10333
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]

RNA

  1. XR_001754317.1 RNA Sequence

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