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    SPTLC1 serine palmitoyltransferase long chain base subunit 1 [ Homo sapiens (human) ]

    Gene ID: 10558, updated on 9-Jun-2024

    Summary

    Official Symbol
    SPTLC1provided by HGNC
    Official Full Name
    serine palmitoyltransferase long chain base subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:11277
    See related
    Ensembl:ENSG00000090054 MIM:605712; AllianceGenome:HGNC:11277
    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
    HSN1; LBC1; LCB1; SPT1; SPTI; ALS27; HSAN1
    Summary
    This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in thyroid (RPKM 21.8), esophagus (RPKM 19.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPTLC1 in Genome Data Viewer
    Location:
    9q22.31
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (92031147..92115413, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104197620..104281900, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94793429..94877695, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 82 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 22 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:94817991-94818611 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94820976-94821830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94865546-94866046 Neighboring gene putative UPF0607 protein FLJ37424 pseudogene Neighboring gene MT-ATP6 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28589 Neighboring gene MT-CO3 pseudogene 29 Neighboring gene MT-ND3 pseudogene 23 Neighboring gene MT-ND4L pseudogene 7 Neighboring gene MT-ND4 pseudogene 15 Neighboring gene protein tyrosine phosphatase receptor type H pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94896185-94896816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94902296-94902875 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94903455-94904034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94904035-94904613 Neighboring gene small nucleolar RNA U13 Neighboring gene long intergenic non-protein coding RNA 475

    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

    EBI GWAS Catalog

    Description
    Genetic variation modifies risk for neurodegeneration based on biomarker status.
    EBI GWAS Catalog
    Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat upregulates serine palmitoyltransferase, long chain base subunit 1 (SPTLC1, SPT1) 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

    • MGC14645

    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
     
    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
    part_of SPOTS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    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
     
    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 1
    Names
    long chain base biosynthesis protein 1
    serine C-palmitoyltransferase
    serine-palmitoyl-CoA transferase 1
    NP_001268232.1
    NP_001355201.1
    NP_001355202.1
    NP_006406.1
    NP_847894.1
    XP_024303146.1
    XP_024303147.1
    XP_047278594.1
    XP_047278595.1
    XP_054217730.1
    XP_054217731.1
    XP_054217732.1
    XP_054217733.1

    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_007950.1 RefSeqGene

      Range
      4935..89275
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_272

    mRNA and Protein(s)

    1. NM_001281303.2NP_001268232.1  serine palmitoyltransferase 1 isoform c

      See identical proteins and their annotated locations for NP_001268232.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 3'-terminal exon, which results in a translational frameshift, compared to variant 1. The encoded isoform (c) has a longer and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK291546, BC068537, DA305642
      UniProtKB/TrEMBL
      Q6NUL7
      Conserved Domains (1) summary
      cl18945
      Location:11442
      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 ...
    2. NM_001368272.1NP_001355201.1  serine palmitoyltransferase 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AL354751, AL391219
    3. NM_001368273.1NP_001355202.1  serine palmitoyltransferase 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL354751, AL391219
      Related
      ENST00000686799.1
      Conserved Domains (1) summary
      cl18945
      Location:1317
      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 ...
    4. NM_006415.4NP_006406.1  serine palmitoyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_006406.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes isoform a.
      Source sequence(s)
      AK291546, BC068537, DA305642
      Consensus CDS
      CCDS6692.1
      UniProtKB/Swiss-Prot
      A8K681, O15269, Q5VWB4, Q96IX6
      UniProtKB/TrEMBL
      A0A8I5QKQ8
      Related
      ENSP00000262554.2, ENST00000262554.7
      Conserved Domains (1) summary
      cl18945
      Location:11472
      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 ...
    5. NM_178324.3NP_847894.1  serine palmitoyltransferase 1 isoform b

      See identical proteins and their annotated locations for NP_847894.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks several exons and its 3'-terminal exon extends past a splice site that is used in variant 1. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AF147304, BC007085, DA305642
      Consensus CDS
      CCDS6693.1
      UniProtKB/TrEMBL
      A0A2R8Y6A2
      Related
      ENSP00000337635.4, ENST00000337841.4
      Conserved Domains (1) summary
      cl18945
      Location:11141
      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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      92031147..92115413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422638.1XP_047278594.1  serine palmitoyltransferase 1 isoform X1

      Related
      ENST00000689261.1
    2. XM_024447379.2XP_024303147.1  serine palmitoyltransferase 1 isoform X3

      Conserved Domains (1) summary
      cl18945
      Location:1317
      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 ...
    3. XM_047422639.1XP_047278595.1  serine palmitoyltransferase 1 isoform X2

    4. XM_024447378.2XP_024303146.1  serine palmitoyltransferase 1 isoform X3

      Conserved Domains (1) summary
      cl18945
      Location:1317
      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 ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      104197620..104281900 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361755.1XP_054217730.1  serine palmitoyltransferase 1 isoform X1

    2. XM_054361758.1XP_054217733.1  serine palmitoyltransferase 1 isoform X3

    3. XM_054361756.1XP_054217731.1  serine palmitoyltransferase 1 isoform X2

    4. XM_054361757.1XP_054217732.1  serine palmitoyltransferase 1 isoform X3

    RNA

    1. XR_008487924.1 RNA Sequence