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Tchem
SPTLC2
Serine palmitoyltransferase 2

Protein Summary
Description
Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate. 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]
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000216484
  • ENSP00000216484
  • ENSG00000100596

Symbol
  • KIAA0526
  • LCB2
  • LCB2
  • SPT2
  • HSN1C
  • LCB2A
  • NSAN1C
  • hLCB2a
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
disease perturbation
1
transcription factor perturbation
0.99
virus perturbation
0.95
microRNA
0.83
transcription factor binding site profile
0.8


Related Tools
Target Illumination GWAS Analytics (TIGA)
TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 80.11   (req: < 5)
Gene RIFs: 10   (req: <= 3)
Antibodies: 255   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 80.11   (req: >= 5)
Gene RIFs: 10   (req: > 3)
Antibodies: 255   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 8
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 1
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Active Ligands (1)
1 – 1 of 1
CHEMBL1241090
chemical structure image
GWAS Traits (1)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
red blood cell distribution width
3
4
4
85.9
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
red blood cell distribution width
4
85.9
Orthologs (15)
1 – 5 of 15
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
serine palmitoyltransferase long chain base subunit 2
VGNC:6775
457898
Macaque
serine palmitoyltransferase long chain base subunit 2
707625
Mouse
MGI:108074
20773
Rat
RGD:1305447
366697
Dog
serine palmitoyltransferase long chain base subunit 2
VGNC:46780
480403
Species
Name
OMA
EggNOG
Inparanoid
Chimp
serine palmitoyltransferase long chain base subunit 2
Macaque
serine palmitoyltransferase long chain base subunit 2
Mouse
Rat
Dog
serine palmitoyltransferase long chain base subunit 2
Protein Structure (0 Structures, 1 AlphaFold Model)
RepresentationColor Scheme
AF-O15270-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

Pathways (20)
Metabolism (R-HSA-1430728)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 4 of 4
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Metabolism
Reactome
Metabolism of lipids
Reactome
Sphingolipid de novo biosynthesis
Reactome
Sphingolipid metabolism
Name
Explore in Pharos
Explore in Source
Metabolism
Metabolism of lipids
Sphingolipid de novo biosynthesis
Sphingolipid metabolism
Protein-Protein Interactions (86)
1 – 10 of 86
FAM241A
Tdark
Novelty: 1.04041354
p_int: 0.954572036
p_ni: 0.045427964
Data Source: BioPlex
SPINT2
Tbio
Family: Enzyme
Novelty: 0.0046602
p_int: 0.88881777
p_ni: 0.11118223
Data Source: BioPlex
TGFA
Tbio
Novelty: 0.00216159
p_int: 0.879569136
p_ni: 0.120430864
Data Source: BioPlex
LRRTM1
Tbio
Novelty: 0.0409182
p_int: 0.848235518
p_ni: 0.151764482
Score: 0.175
Data Source: BioPlex,STRINGDB
EVA1C
Tbio
Novelty: 0.45928677
p_int: 0.839796191
p_ni: 0.160203809
Data Source: BioPlex
ROM1
Tbio
Novelty: 0.0088008
p_int: 0.81147271
p_ni: 0.18852729
Score: 0.685
Data Source: BioPlex,STRINGDB
SPTSSA
Tbio
Family: Enzyme
Novelty: 0.13352078
Score: 0.993
Data Source: Reactome,STRINGDB
SPTSSB
Tdark
Family: Enzyme
Novelty: 0.05967882
Score: 0.993
Data Source: Reactome,STRINGDB
SPTLC1
Tchem
Family: Enzyme
Novelty: 0.00639691
Score: 0.991
Data Source: Reactome,STRINGDB
KDSR
Tbio
Family: Enzyme
Novelty: 0.0408411
Score: 0.971
Data Source: STRINGDB
Publication Statistics
PubMed Score  80.11

PubMed score by year
PubTator Score  25.62

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer
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