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SPTLC2 serine palmitoyltransferase long chain base subunit 2 [ Homo sapiens (human) ]

Gene ID: 9517, updated on 11-Jun-2025
Official Symbol
SPTLC2provided by HGNC
Official Full Name
serine palmitoyltransferase long chain base subunit 2provided by HGNC
Primary source
HGNC:HGNC:11278
See related
Ensembl:ENSG00000100596 MIM:605713; AllianceGenome:HGNC:11278
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
LCB2; SPT2; HSN1C; LCB2A; NSAN1C; hLCB2a
Summary
This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in esophagus (RPKM 11.7), colon (RPKM 11.4) and 25 other tissues See more
Orthologs
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See SPTLC2 in Genome Data Viewer
Location:
14q24.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77505997..77616637, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71715382..71825999, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (77972340..78082980, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77923742-77924264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77924265-77924787 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36801 Neighboring gene activator of HSP90 ATPase activity 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77950905-77951405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77957001-77957502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77957503-77958002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8803 Neighboring gene isthmin 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78008897-78009398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8805 Neighboring gene RNA, 7SL, cytoplasmic 587, pseudogene Neighboring gene MPRA-validated peak2208 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:78072555-78073054 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78073869-78074370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:78074371-78074870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8808 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:78082775-78083307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:78128831-78129662 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 11 Neighboring gene MPRA-validated peak2209 silencer Neighboring gene MPRA-validated peak2210 silencer Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene ribosomal protein L21 pseudogene 10

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat upregulates serine palmitoyltransferase, long chain base subunit 2 (SPTLC2, SPT2) expression in Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Clone Names

  • KIAA0526

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
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
 
contributes_to serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables serine C-palmitoyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to serine C-palmitoyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables serine C-palmitoyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables serine C-palmitoyltransferase activity TAS
Traceable Author Statement
more info
PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in adipose tissue development IEA
Inferred from Electronic Annotation
more info
 
involved_in adipose tissue development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within ceramide biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of lipophagy IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within sphinganine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within sphingolipid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sphingolipid biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sphingolipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
involved_in sphingolipid metabolic process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within sphingomyelin biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in sphingosine biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within sphingosine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingosine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
 
part_of serine palmitoyltransferase complex IPI
Inferred from Physical Interaction
more info
PubMed 
Preferred Names
serine palmitoyltransferase 2
Names
LCB 2
SPT 2
long chain base biosynthesis protein 2a
serine palmitoyltransferase, subunit II
serine-palmitoyl-CoA transferase 2
NP_004854.1
XP_011535686.1
XP_054233063.1

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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_028282.1 RefSeqGene

    Range
    5001..115771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_371

mRNA and Protein(s)

  1. NM_004863.4NP_004854.1  serine palmitoyltransferase 2

    See identical proteins and their annotated locations for NP_004854.1

    Status: REVIEWED

    Source sequence(s)
    AB011098, AF111168, BQ338973
    Consensus CDS
    CCDS9865.1
    UniProtKB/Swiss-Prot
    O15270, Q16685
    Related
    ENSP00000216484.2, ENST00000216484.7
    Conserved Domains (1) summary
    cl18945
    Location:67542
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    77505997..77616637 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537384.3XP_011535686.1  serine palmitoyltransferase 2 isoform X1

    See identical proteins and their annotated locations for XP_011535686.1

    UniProtKB/TrEMBL
    H0YJV2
    Related
    ENSP00000452189.1, ENST00000554901.1
    Conserved Domains (2) summary
    PLN02483
    Location:67435
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:117426
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    71715382..71825999 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377088.1XP_054233063.1  serine palmitoyltransferase 2 isoform X1

    UniProtKB/TrEMBL
    H0YJV2