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

Gene ID: 9517, updated on 11-Jun-2021

Summary

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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
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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Genomic context

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See SPTLC2 in Genome Data Viewer
Location:
14q24.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (77505997..77616663, complement)
105.20201022 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 activator of HSP90 ATPase activity 1 Neighboring gene isthmin 2 Neighboring gene RNA, 7SL, cytoplasmic 587, pseudogene Neighboring gene cytochrome c oxidase subunit 6C pseudogene 11 Neighboring gene alkB homolog 1, histone H2A dioxygenase Neighboring gene ribosomal protein L21 pseudogene 10

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. A Novel Variant (Asn177Asp) in SPTLC2 Causing Hereditary Sensory Autonomic Neuropathy Type 1C. Suriyanarayanan S, et al. Neuromolecular Med, 2019 Jun. PMID 30955194
  2. The pyridoxal 5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT): effects of the small subunits and insights from bacterial mimics of human hLCB2a HSAN1 mutations. Beattie AE, et al. Biomed Res Int, 2013. PMID 24175284, Free PMC Article
  3. Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2. Murphy SM, et al. Neurology, 2013 Jun 4. PMID 23658386, Free PMC Article
  4. Exclusion of serine palmitoyltransferase long chain base subunit 2 (SPTLC2) as a common cause for hereditary sensory neuropathy. Dawkins JL, et al. Neuromuscul Disord, 2002 Oct. PMID 12207934
  5. Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease. Ban GY, et al. PLoS One, 2020. PMID 33031402, Free PMC Article

See all (59) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
    Title: Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
  2. A Novel Variant (Asn177Asp) in SPTLC2 Causing Hereditary Sensory Autonomic Neuropathy Type 1C.
    Title: A Novel Variant (Asn177Asp) in SPTLC2 Causing Hereditary Sensory Autonomic Neuropathy Type 1C.
  3. Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease.
    Title: Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease.
  4. Elevated levels of atypical deoxysphingolipids, caused by variant SPTLC1 or SPTLC2 or by low serine levels, were risk factors for macular telangiectasia type 2, as well as for peripheral neuropathy.
    Title: Serine and Lipid Metabolism in Macular Disease and Peripheral Neuropathy.
  5. HSAN-I-associated mutations in serine palmitoyltransferase subunit SPTLC2 dampened human T cell responses. SPTLC2 underpins protective immunity by translating extracellular stimuli into intracellular anabolic signals and antagonizes endoplasmic reticulum stress to promote T cell metabolic fitness.
    Title: Loss of Neurological Disease HSAN-I-Associated Gene SPTLC2 Impairs CD8<sup>+</sup> T Cell Responses to Infection by Inhibiting T Cell Metabolic Fitness.
  6. 2 families had late-onset autosomal dominant HSAN1C caused by a new variant in SPTLC2, c.547C>T, p.(Arg183Trp). The variant changed a conserved amino acid.
    Title: The Variant p.(Arg183Trp) in SPTLC2 Causes Late-Onset Hereditary Sensory Neuropathy.
  7. The activities of the hLCB2a mutants were measured in the presence of ssSPTa and ssSPTb and was found that all decrease enzyme activity.
    Title: The pyridoxal 5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT): effects of the small subunits and insights from bacterial mimics of human hLCB2a HSAN1 mutations.
  8. Mutations in SPTLC2 are associated with increased deoxySL formation causing hereditary sensory and autonomic neuropathy type 1 (HSANI) in a familial study.
    Title: Hereditary sensory and autonomic neuropathy type 1 (HSANI) caused by a novel mutation in SPTLC2.
  9. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  10. Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.
    Title: Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hereditary sensory and autonomic neuropathy type IC
MedGen: C3150896 OMIM: 613640 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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
 PubMed 
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 
Process Evidence Code Pubs
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
 PubMed 
acts_upstream_of_or_within ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within positive regulation of lipophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in 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 TAS
Traceable Author Statement
more info
 PubMed 
involved_in sphingomyelin biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in sphingosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
  
part_of serine C-palmitoyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
part_of serine C-palmitoyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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

NCBI Reference Sequences (RefSeq)

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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_004863.4 → NP_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
    UniProtKB/TrEMBL
    A0A024R6H1
    Related
    ENSP00000216484.2, ENST00000216484.7
    Conserved Domains (1) summary
    PLN02483
    Location:67 → 542
    PLN02483; serine palmitoyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    77505997..77616663 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_011535686.1

    Related
    ENSP00000452189.1, ENST00000554901.1
    Conserved Domains (2) summary
    PLN02483
    Location:67 → 435
    PLN02483; serine palmitoyltransferase
    COG0156
    Location:117 → 426
    BioF; 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15270.1 GenPept UniProtKB/Swiss-Prot:O15270

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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