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

Gene ID: 10558, updated on 4-May-2020

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
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]
Expression
Ubiquitous expression in thyroid (RPKM 21.8), esophagus (RPKM 19.8) and 25 other tissues See more
Orthologs

Genomic context

See SPTLC1 in Genome Data Viewer
Location:
9q22.31
Exon count:
20
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (92031141..92115413, 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 putative UPF0607 protein FLJ37424 pseudogene Neighboring gene MT-ATP6 pseudogene 29 Neighboring gene MT-CO3 pseudogene 29 Neighboring gene MT-ND3 pseudogene 23 Neighboring gene MT-ND4 pseudogene 15 Neighboring gene protein tyrosine phosphatase pseudogene Neighboring gene uncharacterized LOC112268047 Neighboring gene Sharpr-MPRA regulatory region 423 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

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

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

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
Process Evidence Code Pubs
ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of lipophagy IDA
Inferred from Direct Assay
more info
PubMed 
regulation of fat cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
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 

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_011516440.1
XP_016869690.1
XP_024303146.1
XP_024303147.1

NCBI Reference Sequences (RefSeq)

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/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_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
  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
    O15269
    UniProtKB/TrEMBL
    A0A024R277, Q6NUL7
    Related
    ENSP00000262554.2, ENST00000262554.7
    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 ...
  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/Swiss-Prot
    O15269
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    92031141..92115413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014201.2XP_016869690.1  serine palmitoyltransferase 1 isoform X2

  2. XM_024447379.1XP_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_024447378.1XP_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 ...
  4. XM_011518138.2XP_011516440.1  serine palmitoyltransferase 1 isoform X1

    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 ...
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