SHMT2 [The Human Chemical-Genetic Interaction Map Project]

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======= SHMT2 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: SHMT2
  * **<color #00a2e8>Official Name</color>**: serine hydroxymethyltransferase 2
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=6472|6472]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/P34897|P34897]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=SHMT2&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20SHMT2|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/138450|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism. Thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Interconversion of serine and glycine (PubMed:25619277). Associates with mitochondrial DNA (PubMed:18063578). Plays a role in the deubiquitination of target proteins as component of the BRISC complex (PubMed:24075985). Required for IFNAR1 deubiquitination by the BRISC complex (PubMed:24075985). {ECO:0000269|PubMed:18063578, ECO:0000269|PubMed:21876188, ECO:0000269|PubMed:24075985, ECO:0000269|PubMed:25619277}.

<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'>
|SHMT|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|L-allo-threonine aldolase activity|
|glycine biosynthetic process from serine|
|cellular response to tetrahydrofolate|
|response to tetrahydrofolate|
|glycine hydroxymethyltransferase activity|
|cobalt ion binding|
|glycine biosynthetic process|
|serine binding|
|BRISC complex|
|L-serine catabolic process|
|L-serine biosynthetic process|
|regulation of aerobic respiration|
|tetrahydrofolate interconversion|
|L-serine metabolic process|
|serine family amino acid catabolic process|
|serine family amino acid biosynthetic process|
|amino acid binding|
|glycine metabolic process|
|tetrahydrofolate metabolic process|
|folic acid metabolic process|
|regulation of mitochondrial translation|
|one-carbon metabolic process|
|regulation of mitochondrial gene expression|
|folic acid-containing compound metabolic process|
|regulation of cellular respiration|
|regulation of oxidative phosphorylation|
|protein K63-linked deubiquitination|
|pteridine-containing compound metabolic process|
|serine family amino acid metabolic process|
|neurotransmitter biosynthetic process|
|mitochondrial nucleoid|
|pyridoxal phosphate binding|
|alpha-amino acid biosynthetic process|
|response to type I interferon|
|mitochondrial intermembrane space|
|cellular amino acid biosynthetic process|
|water-soluble vitamin metabolic process|
|neurotransmitter metabolic process|
|protein homotetramerization|
|dicarboxylic acid metabolic process|
|alpha-amino acid catabolic process|
|regulation of ATP metabolic process|
|vitamin metabolic process|
|cellular amino acid catabolic process|
|protein tetramerization|
|microtubule cytoskeleton|
|regulation of generation of precursor metabolites and energy|
|cellular modified amino acid metabolic process|
|cellular response to acid chemical|
|alpha-amino acid metabolic process|
|coenzyme metabolic process|
|carboxylic acid catabolic process|
|organic acid catabolic process|
|protein deubiquitination|
|protein modification by small protein removal|
|carboxylic acid biosynthetic process|
|organic acid biosynthetic process|
|cellular amino acid metabolic process|
|protein homooligomerization|
|response to acid chemical|
|regulation of translation|
|regulation of neurotransmitter levels|
|mitochondrial matrix|
|chromatin binding|
|mitochondrial inner membrane|
|regulation of cellular amide metabolic process|
|small molecule catabolic process|
|cofactor metabolic process|
|drug metabolic process|
|protein complex oligomerization|
|posttranscriptional regulation of gene expression|
|cellular response to organic cyclic compound|
|small molecule biosynthetic process|
|cellular response to organonitrogen compound|
|cellular response to nitrogen compound|
|innate immune response|
|cellular amide metabolic process|
|zinc ion binding|
|carboxylic acid metabolic process|
|positive regulation of cell population proliferation|
|response to organic cyclic compound|
|defense response to other organism|
|protein modification by small protein conjugation or removal|
|response to organonitrogen compound|
|oxoacid metabolic process|
|organic acid metabolic process|
|cellular response to oxygen-containing compound|
|organonitrogen compound catabolic process|
|identical protein binding|
|response to nitrogen compound|
|response to cytokine|
|cellular response to endogenous stimulus|
|mitochondrion|
|proteolysis|
|response to other organism|
|response to external biotic stimulus|
|response to biotic stimulus|
|defense response|
|organonitrogen compound biosynthetic process|
|response to endogenous stimulus|
|response to oxygen-containing compound|
|protein-containing complex assembly|
|regulation of phosphorylation|
|regulation of cell population proliferation|
|small molecule metabolic process|
|organic substance catabolic process|
|regulation of phosphate metabolic process|
|regulation of phosphorus metabolic process|
|cellular catabolic process|
|protein-containing complex subunit organization|
|immune response|
</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:exp501|Methotrexate 0.01μM R08 exp501]]|-2.28|
|[[:results:exp356|Docosahexaenoic-acid 50μM R07 exp356]]|1.7|
|[[:results:exp346|CoCl2 18μM R07 exp346]]|1.72|
|[[:results:exp288|HMS-I2 10μM R06 exp288]]|1.73|
|[[:results:exp287|HMS-I2 5μM R06 exp287]]|1.73|
|[[:results:exp269|Bisphenol A 100μM R06 exp269]]|1.74|
|[[:results:exp30|Rapamycin 10μM R00 exp30]]|1.77|
|[[:results:exp504|MK2206 4μM R08 exp504]]|1.78|
|[[:results:exp69|Deguelin 0.05μM R02 exp69]]|1.81|
|[[:results:exp68|Clomiphene 4.4μM R02 exp68]]|1.82|
|[[:results:exp240|Pyridostatin 4μM R05 exp240]]|1.82|
|[[:results:exp415|Trichostatin-A 0.06μM R07 exp415]]|1.86|
|[[:results:exp468|CB-5083 0.4μM R08 exp468]]|1.88|
|[[:results:exp529|Thimerosal 0.85μM R08 exp529]]|1.92|
|[[:results:exp446|4-Nitroquinoline-1-oxide 0.5μM R08 exp446]]|1.96|
|[[:results:exp457|Bisphenol F 50μM R08 exp457]]|1.97|
|[[:results:exp433|LJH685 50μM R08 exp433]]|1.97|
|[[:results:exp360|Genistein 15μM R07 exp360]]|2.05|
|[[:results:exp212|Phenformin 20μM R05 exp212]]|2.05|
|[[:results:exp490|Hydroxychloroquine 30μM R08 exp490]]|2.07|
|[[:results:exp492|iCRT14 30μM R08 exp492]]|2.09|
|[[:results:exp399|Salubrinal 20μM R07 exp399]]|2.09|
|[[:results:exp465|Cannabidiol 13μM R08 exp465]]|2.13|
|[[:results:exp400|Senexin-A 25μM R07 exp400]]|2.17|
|[[:results:exp475|CyclicAMP 200μM R08 exp475]]|2.2|
|[[:results:exp530|Thioridazine 5μM R08 exp530]]|2.24|
|[[:results:exp461|BS-181 20μM R08 exp461]]|2.25|
|[[:results:exp454|Bafilomycin-A1 0.009μM R08 exp454]]|2.3|
|[[:results:exp380|NMS-873 0.07μM R07 exp380]]|2.4|
|[[:results:exp498|Lead acetate 2000μM R08 exp498 no dilution day6]]|2.41|
|[[:results:exp455|Benzoate 10000μM R08 exp455]]|2.43|
|[[:results:exp520|Rucaparib 6.5μM R08 exp520]]|2.49|
|[[:results:exp248|UM0131023 0.05μM R05 exp248]]|2.51|
|[[:results:exp447|Amiloride 100μM R08 exp447]]|2.56|
|[[:results:exp535|Trimetrexate 0.03μM R08 exp535]]|2.56|
|[[:results:exp483|FTY720 3μM R08 exp483]]|2.58|
|[[:results:exp470|Chloroquine 32μM R08 exp470]]|2.6|
|[[:results:exp431|Rotenone 0.07μM R08 exp431]]|2.64|
|[[:results:exp227|Cryptotanshinone 12μM R05 exp227]]|3.09|
|[[:results:exp453|B02 10μM R08 exp453]]|3.13|
|[[:results:exp191|Hypoxia 5%O2 R04 exp191]]|3.21|
|[[:results:exp439|QNZ 0.01μM R08 exp439]]|3.34|
|[[:results:exp116|AICAR 240μM R03 exp116]]|5.14|
|[[:results:exp211|AICAR 240μM R05 exp211]]|5.57|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:s:slc25a32|SLC25A32]]|0.641|
|[[:human genes:m:mthfd1l|MTHFD1L]]|0.615|
|[[:human genes:m:mthfd2|MTHFD2]]|0.572|
|[[:human genes:p:polr2j3|POLR2J3]]|0.47|
|[[:human genes:m:mtr|MTR]]|0.458|
|[[:human genes:m:mmachc|MMACHC]]|0.454|
|[[:human genes:m:mtrr|MTRR]]|0.417|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 2/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|1/28|
|blood|0/28|
|bone|0/26|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/16|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/16|
|ovary|0/26|
|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>**: 1375
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.57 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='SHMT2 Expression in NALM6 Cells: 7.57'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>