SPTLC1 [The Human Chemical-Genetic Interaction Map Project]

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======= SPTLC1 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: SPTLC1
  * **<color #00a2e8>Official Name</color>**: serine palmitoyltransferase long chain base subunit 1
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=10558|10558]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/O15269|O15269]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=SPTLC1&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20SPTLC1|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/605712|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  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]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 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-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1- SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference. {ECO:0000269|PubMed:19416851}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|Aminotran 1 2|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|sphinganine biosynthetic process|
|regulation of fat cell apoptotic process|
|sphinganine metabolic process|
|SPOTS complex|
|serine C-palmitoyltransferase complex|
|serine C-palmitoyltransferase activity|
|positive regulation of lipophagy|
|regulation of lipophagy|
|sphingomyelin biosynthetic process|
|sphingosine biosynthetic process|
|sphingoid biosynthetic process|
|sphingosine metabolic process|
|sphingomyelin metabolic process|
|sphingoid metabolic process|
|diol biosynthetic process|
|diol metabolic process|
|ceramide biosynthetic process|
|pyridoxal phosphate binding|
|polyol biosynthetic process|
|positive regulation of macroautophagy|
|ceramide metabolic process|
|sphingolipid biosynthetic process|
|polyol metabolic process|
|alcohol biosynthetic process|
|positive regulation of autophagy|
|membrane lipid biosynthetic process|
|sphingolipid metabolic process|
|regulation of macroautophagy|
|organic hydroxy compound biosynthetic process|
|ammonium ion metabolic process|
|membrane lipid metabolic process|
|phospholipid biosynthetic process|
|alcohol metabolic process|
|regulation of autophagy|
|positive regulation of cellular catabolic process|
|phospholipid metabolic process|
|positive regulation of catabolic process|
|organic hydroxy compound metabolic process|
|amide biosynthetic process|
|organophosphate biosynthetic process|
|lipid biosynthetic process|
|small molecule biosynthetic process|
|cellular amide metabolic process|
|regulation of cellular catabolic process|
|organophosphate metabolic process|
|endoplasmic reticulum membrane|
|cellular lipid metabolic process|
|regulation of catabolic process|
|endoplasmic reticulum|
|lipid metabolic process|
|organonitrogen compound biosynthetic process|
|regulation of apoptotic process|
|regulation of programmed cell death|
|cellular nitrogen compound biosynthetic process|
|regulation of cell death|
|small molecule metabolic process|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp90|WYE-354 6μM R02 exp90]]|-4.36|
|[[:results:exp169|BH1 1μM R04 exp169]]|-4.18|
|[[:results:exp538|ZLN024 50μM R08 exp538]]|-4.04|
|[[:results:exp506|Momordin-Ic 10μM R08 exp506]]|-3.77|
|[[:results:exp89|Vemurafenib 6.6μM R02 exp89]]|-3.72|
|[[:results:exp434|Vemurafenib 6.6μM R08 exp434]]|-3.62|
|[[:results:exp164|Q15 1 to 2μM on day4 R04 exp164]]|-3.18|
|[[:results:exp47|Lapatinib 5μM R01 exp47]]|-3.13|
|[[:results:exp68|Clomiphene 4.4μM R02 exp68]]|-3.08|
|[[:results:exp461|BS-181 20μM R08 exp461]]|-2.87|
|[[:results:exp233|EPZ-5676 30μM R05 exp233]]|-2.87|
|[[:results:exp78|Pterostilbene 16μM R02 exp78]]|-2.32|
|[[:results:exp416|Tubacin 1.6μM R07 exp416]]|-2.23|
|[[:results:exp444|THZ531 0.225μM R08 exp444]]|-2.2|
|[[:results:exp507|Monensin 0.3μM R08 exp507]]|-2.14|
|[[:results:exp131|L-74142 5μM R03 exp131]]|-2.06|
|[[:results:exp422|Wiskostatin 3μM R07 exp422]]|-1.95|
|[[:results:exp445|∆-9-Tetrahydrocannabinol 30μM R08 exp445]]|-1.92|
|[[:results:exp234|Ethanol 0.01 R05 exp234]]|-1.91|
|[[:results:exp539|42°C R08 exp539]]|-1.88|
|[[:results:exp149|SB203580 25μM R03 exp149]]|-1.75|
|[[:results:exp436|Dynasore 7μM R08 exp436]]|-1.74|
|[[:results:exp536|Vitamin-D3 40μM R08 exp536]]|-1.74|
|[[:results:exp151|SGC0946 7μM R03 exp151]]|-1.73|
|[[:results:exp45|Docetaxel 0.002μM R01 exp45]]|-1.71|
|[[:results:exp407|Thapsigargin 0.005μM R07 exp407]]|-1.71|
|[[:results:exp514|Phorbol-12-myristate-13-acetate 0.57μM R08 exp514]]|2.09|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:s:sptlc2|SPTLC2]]|0.634|
|[[:human genes:s:sptssa|SPTSSA]]|0.561|
|[[:human genes:c:col4a3bp|COL4A3BP]]|0.56|
|[[:human genes:s:sgms1|SGMS1]]|0.481|
|[[:human genes:g:gpr107|GPR107]]|0.473|
|[[:human genes:c:chka|CHKA]]|0.471|
|[[:human genes:c:c10orf76|C10orf76]]|0.451|
|[[:human genes:a:arl1|ARL1]]|0.442|
|[[:human genes:v:vkorc1l1|VKORC1L1]]|0.425|
|[[:human genes:m:mbtps1|MBTPS1]]|0.424|
|[[:human genes:c:cog7|COG7]]|0.415|
|[[:human genes:f:flvcr1|FLVCR1]]|0.414|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 18/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|1/28|
|bone|0/26|
|breast|0/33|
|central nervous system|1/56|
|cervix|0/4|
|colorectal|1/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/16|
|kidney|0/21|
|liver|0/20|
|lung|3/75|
|lymphocyte|2/16|
|ovary|1/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/9|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 6735
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.14 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='SPTLC1 Expression in NALM6 Cells: 6.14'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>