Format

Send to:

Choose Destination

Links from PubMed

    • Showing Current items.

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

    Gene ID: 10558, updated on 21-Dec-2016
    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; Vega:OTTHUMG00000021047
    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; 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]
    Orthologs
    Location:
    9q22.31
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (92031134..92115474, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94793416..94877756, 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 UPF0607 protein ENSP00000381418-like pseudogene Neighboring gene mitochondrially encoded ATP synthase 6 pseudogene 29 Neighboring gene mitochondrially encoded cytochrome c oxidase III pseudogene 29 Neighboring gene mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 pseudogene 23 Neighboring gene mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 pseudogene 15 Neighboring gene protein tyrosine phosphatase pseudogene Neighboring gene long intergenic non-protein coding RNA 475

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC14645

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    serine C-palmitoyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to serine C-palmitoyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    serine C-palmitoyltransferase activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    ceramide biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of lipophagy IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sphinganine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    sphingolipid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
    PubMed 
    sphingolipid metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    sphingomyelin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    sphingosine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    SPOTS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    serine C-palmitoyltransferase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    serine palmitoyltransferase 1
    Names
    LCB 1
    SPT 1
    long chain base biosynthesis protein 1
    serine C-palmitoyltransferase
    serine-palmitoyl-CoA transferase 1
    NP_001268232.1
    NP_006406.1
    NP_847894.1

    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_001281303.1NP_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, EC564300
      UniProtKB/Swiss-Prot
      O15269
      UniProtKB/TrEMBL
      Q6NUL7
      Conserved Domains (2) summary
      pfam00155
      Location:98445
      Aminotran_1_2; Aminotransferase class I and II
      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_006415.3NP_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, EC564300
      Consensus CDS
      CCDS6692.1
      UniProtKB/Swiss-Prot
      O15269
      UniProtKB/TrEMBL
      A0A024R277, Q6NUL7
      Related
      ENSP00000262554, OTTHUMP00000022810, ENST00000262554, OTTHUMT00000055553
      Conserved Domains (2) summary
      COG0156
      Location:93467
      BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
      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 ...
    3. NM_178324.2NP_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/Swiss-Prot
      O15269
      Related
      ENSP00000337635, OTTHUMP00000022811, ENST00000337841, OTTHUMT00000055554
      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: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      92031134..92115474 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014200.1XP_016869689.1  

    2. XM_011518139.2XP_011516441.1  

      Conserved Domains (2) summary
      COG0156
      Location:2312
      BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
      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_017014201.1XP_016869690.1  

    4. XM_017014202.1XP_016869691.1  

    5. XM_011518138.2XP_011516440.1  

      Conserved Domains (2) summary
      COG0156
      Location:93362
      BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
      cl18945
      Location:11363
      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 ...

    RNA

    1. XR_001746159.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      94939836..95024218 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center