U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 9517, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPTLC2 in Genome Data Viewer
    Location:
    14q24.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (77505997..77616637, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (71715382..71825999, complement)
    105.20220307 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

    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?

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0526

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 
    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 C-palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_2023_10

    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