Details for: SHMT1

Gene ID: 6470

Symbol: SHMT1

Ensembl ID: ENSG00000176974

Description: serine hydroxymethyltransferase 1

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: polychromatophilic erythroblast (CL0000550)
    Fold Change: 108.8751
    Cell Significance Index: -16.9400
  • Cell Name: hematopoietic oligopotent progenitor cell (CL0002032)
    Fold Change: 71.3009
    Cell Significance Index: -18.0900
  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 43.3592
    Cell Significance Index: -17.6200
  • Cell Name: orthochromatic erythroblast (CL0000552)
    Fold Change: 15.7548
    Cell Significance Index: -19.4300
  • Cell Name: periportal region hepatocyte (CL0019026)
    Fold Change: 8.9116
    Cell Significance Index: 131.5400
  • Cell Name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell (CL0000796)
    Fold Change: 6.4318
    Cell Significance Index: -17.2300
  • Cell Name: stromal cell of bone marrow (CL0010001)
    Fold Change: 5.0456
    Cell Significance Index: -19.9100
  • Cell Name: centrilobular region hepatocyte (CL0019029)
    Fold Change: 3.3503
    Cell Significance Index: 56.4400
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 3.2274
    Cell Significance Index: 614.1900
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 2.4178
    Cell Significance Index: 167.2100
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 2.2422
    Cell Significance Index: 221.8100
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 1.2272
    Cell Significance Index: 199.6000
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 1.0521
    Cell Significance Index: 208.8000
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: 0.9422
    Cell Significance Index: 26.3300
  • Cell Name: thyroid follicular cell (CL0002258)
    Fold Change: 0.7313
    Cell Significance Index: 7.7700
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: 0.6233
    Cell Significance Index: 29.0600
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.5188
    Cell Significance Index: 11.2400
  • Cell Name: neutrophil progenitor cell (CL0000834)
    Fold Change: 0.4826
    Cell Significance Index: 12.9100
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 0.4794
    Cell Significance Index: 261.8200
  • Cell Name: liver dendritic cell (CL2000055)
    Fold Change: 0.4246
    Cell Significance Index: 1.1200
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: 0.3129
    Cell Significance Index: 38.4800
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: 0.3082
    Cell Significance Index: 55.5600
  • Cell Name: sebum secreting cell (CL0000317)
    Fold Change: 0.2877
    Cell Significance Index: 20.3500
  • Cell Name: basal cell of prostate epithelium (CL0002341)
    Fold Change: 0.2711
    Cell Significance Index: 7.3800
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: 0.2680
    Cell Significance Index: 53.7600
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: 0.2579
    Cell Significance Index: 30.4100
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: 0.2423
    Cell Significance Index: 7.7600
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 0.2420
    Cell Significance Index: 6.0500
  • Cell Name: hair follicular keratinocyte (CL2000092)
    Fold Change: 0.2235
    Cell Significance Index: 98.8200
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: 0.1564
    Cell Significance Index: 3.3300
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 0.1545
    Cell Significance Index: 8.6700
  • Cell Name: corneal epithelial cell (CL0000575)
    Fold Change: 0.1426
    Cell Significance Index: 2.0300
  • Cell Name: lactocyte (CL0002325)
    Fold Change: 0.1386
    Cell Significance Index: 17.9100
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: 0.1236
    Cell Significance Index: 44.3300
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 0.1230
    Cell Significance Index: 85.1000
  • Cell Name: mesonephric nephron tubule epithelial cell (CL1000022)
    Fold Change: 0.1068
    Cell Significance Index: 3.7100
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.0895
    Cell Significance Index: 168.5400
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: 0.0701
    Cell Significance Index: 3.6400
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 0.0672
    Cell Significance Index: 42.6800
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: 0.0635
    Cell Significance Index: 97.7100
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: 0.0589
    Cell Significance Index: 108.6400
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.0574
    Cell Significance Index: 2.6000
  • Cell Name: Hofbauer cell (CL3000001)
    Fold Change: 0.0429
    Cell Significance Index: 0.3500
  • Cell Name: cerebellar granule cell (CL0001031)
    Fold Change: 0.0344
    Cell Significance Index: 0.5900
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: 0.0281
    Cell Significance Index: 38.1500
  • Cell Name: pulmonary alveolar epithelial cell (CL0000322)
    Fold Change: 0.0084
    Cell Significance Index: 6.3900
  • Cell Name: pro-T cell (CL0000827)
    Fold Change: 0.0078
    Cell Significance Index: 0.2000
  • Cell Name: subcutaneous adipocyte (CL0002521)
    Fold Change: 0.0023
    Cell Significance Index: 0.0100
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: 0.0007
    Cell Significance Index: 0.5000
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0003
    Cell Significance Index: 0.0100
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.0100
    Cell Significance Index: -1.0200
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0110
    Cell Significance Index: -5.0100
  • Cell Name: epithelial cell of proximal tubule (CL0002306)
    Fold Change: -0.0118
    Cell Significance Index: -0.0900
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.0133
    Cell Significance Index: -1.9400
  • Cell Name: odontoblast (CL0000060)
    Fold Change: -0.0186
    Cell Significance Index: -2.3800
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0302
    Cell Significance Index: -22.3600
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: -0.0307
    Cell Significance Index: -0.8200
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: -0.0329
    Cell Significance Index: -4.5200
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0388
    Cell Significance Index: -21.9000
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: -0.0447
    Cell Significance Index: -0.6100
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0555
    Cell Significance Index: -15.9600
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: -0.0619
    Cell Significance Index: -7.2100
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.0757
    Cell Significance Index: -3.5600
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.0778
    Cell Significance Index: -5.8000
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: -0.0792
    Cell Significance Index: -13.5200
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.0803
    Cell Significance Index: -6.3600
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.1102
    Cell Significance Index: -12.6300
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.1120
    Cell Significance Index: -23.5800
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.1380
    Cell Significance Index: -14.3700
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: -0.1473
    Cell Significance Index: -9.5000
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: -0.1488
    Cell Significance Index: -2.4900
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: -0.1508
    Cell Significance Index: -4.3500
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: -0.1613
    Cell Significance Index: -12.3800
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.2244
    Cell Significance Index: -11.7800
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: -0.2303
    Cell Significance Index: -6.0600
  • Cell Name: hepatoblast (CL0005026)
    Fold Change: -0.2313
    Cell Significance Index: -3.8900
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: -0.2631
    Cell Significance Index: -11.6400
  • Cell Name: CD4-positive, alpha-beta memory T cell, CD45RO-positive (CL0001204)
    Fold Change: -0.2734
    Cell Significance Index: -8.0300
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: -0.2770
    Cell Significance Index: -17.4600
  • Cell Name: OFF midget ganglion cell (CL4033047)
    Fold Change: -0.3120
    Cell Significance Index: -3.8900
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: -0.3155
    Cell Significance Index: -15.9400
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: -0.3216
    Cell Significance Index: -12.1800
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: -0.3287
    Cell Significance Index: -17.1200
  • Cell Name: adipocyte of breast (CL0002617)
    Fold Change: -0.3288
    Cell Significance Index: -4.1400
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: -0.3380
    Cell Significance Index: -20.7200
  • Cell Name: L5 extratelencephalic projecting glutamatergic cortical neuron (CL4023041)
    Fold Change: -0.3471
    Cell Significance Index: -12.1600
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: -0.3546
    Cell Significance Index: -10.4500
  • Cell Name: paneth cell of colon (CL0009009)
    Fold Change: -0.3597
    Cell Significance Index: -5.3900
  • Cell Name: stratified epithelial cell (CL0000079)
    Fold Change: -0.3650
    Cell Significance Index: -13.4000
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: -0.3770
    Cell Significance Index: -7.8200
  • Cell Name: umbrella cell of urothelium (CL4030056)
    Fold Change: -0.3817
    Cell Significance Index: -3.5200
  • Cell Name: fibroblast of dermis (CL0002551)
    Fold Change: -0.3827
    Cell Significance Index: -8.0100
  • Cell Name: ON midget ganglion cell (CL4033046)
    Fold Change: -0.3962
    Cell Significance Index: -5.0000
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.4005
    Cell Significance Index: -13.1100
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: -0.4015
    Cell Significance Index: -10.3200
  • Cell Name: leptomeningeal cell (CL0000708)
    Fold Change: -0.4047
    Cell Significance Index: -8.6500
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: -0.4210
    Cell Significance Index: -11.2800
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.4211
    Cell Significance Index: -13.4100
  • Cell Name: Purkinje cell (CL0000121)
    Fold Change: -0.4466
    Cell Significance Index: -9.7800
  • Cell Name: lamp5 GABAergic cortical interneuron (CL4023011)
    Fold Change: -0.4920
    Cell Significance Index: -10.6300

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics** SHMT1 exhibits several key characteristics that distinguish it from other genes: 1. **Enzyme specificity**: SHMT1 is a cytosolic enzyme that specifically catalyzes the conversion of serine to glycine and 5,10-CH2THF. 2. **Folate synthesis**: SHMT1 plays a critical role in the folate synthesis pathway, which is essential for DNA synthesis, repair, and methylation. 3. **Translation regulation**: SHMT1 has been shown to regulate translation by binding to mRNA regulatory elements and inhibiting protein translation. 4. **Protein binding**: SHMT1 exhibits high-affinity binding to various proteins, including pyridoxal phosphate, serine, and glycine. **Pathways and Functions** SHMT1 is involved in several cellular pathways, including: 1. **Folate synthesis**: SHMT1 catalyzes the conversion of serine to glycine and 5,10-CH2THF, which is then used to synthesize tetrahydrofolate (THF). 2. **Glycine biosynthesis**: SHMT1 is involved in the biosynthesis of glycine from serine, which is a crucial amino acid for various cellular processes. 3. **Translation regulation**: SHMT1 regulates protein translation by binding to mRNA regulatory elements and inhibiting protein translation. 4. **Cellular response to tetrahydrofolate**: SHMT1 is involved in the cellular response to THF, which is essential for DNA synthesis, repair, and methylation. **Clinical Significance** SHMT1 has significant clinical implications, particularly in the context of folate metabolism and DNA synthesis. Abnormalities in SHMT1 expression or function have been linked to various diseases, including: 1. **Folate deficiency**: SHMT1 deficiency can lead to folate deficiency, which can cause megaloblastic anemia, neural tube defects, and other developmental abnormalities. 2. **Cancer**: SHMT1 overexpression has been linked to various types of cancer, including colorectal, breast, and prostate cancer. 3. **Neurological disorders**: SHMT1 has been implicated in the pathogenesis of neurological disorders, such as Alzheimer's disease and Parkinson's disease. In conclusion, SHMT1 is a critical gene that plays a pivotal role in various cellular processes, including metabolism, folate synthesis, and translation regulation. Its clinical significance cannot be overstated, particularly in the context of folate metabolism and DNA synthesis. Further research is needed to fully elucidate the functions and implications of SHMT1 in human health and disease.

Genular Protein ID: 2488436585

Symbol: GLYC_HUMAN

Name: Serine hydroxymethyltransferase, cytosolic

UniProtKB Accession Codes:

P34896 B4DPM9 D3DXD0 Q96HY0 Q9UMD1 Q9UMD2

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 BRENDA 1 Bgee 1 BindingDB 1 BioCyc 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 3 CDD 1 CORUM 1 CTD 1 ChEBI 6 ChEMBL 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 DrugBank 7 DrugCentral 1 EC 1 EMBL 16 EMDB 1 Ensembl 6 EvolutionaryTrace 1 ExpressionAtlas 1 GO 29 Gene3D 2 GeneCards 1 GeneTree 1 GenomeRNAi 1 HAMAP 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 7 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 MoonProt 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 6 PDBsum 6 PIR 1 PIRSF 1 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 4 Pumba 1 RNAct 1 Reactome 2 RefSeq 7 Rhea 1 SABIO-RK 1 SIGNOR 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 UniPathway 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 8505317

Title: Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization.

PubMed ID: 8505317

DOI: 10.1016/s0021-9258(19)50286-1

PubMed ID: 9056951

Title: Isolation and characterisation of human genomic sequences encoding cytosolic serine hydroxymethyltransferase.

PubMed ID: 9056951

DOI: 10.1042/bst025053s

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 16625196

Title: DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PubMed ID: 16625196

DOI: 10.1038/nature04689

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 19608861

Title: Lysine acetylation targets protein complexes and co-regulates major cellular functions.

PubMed ID: 19608861

DOI: 10.1126/science.1175371

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 24075985

Title: A BRISC-SHMT complex deubiquitinates IFNAR1 and regulates interferon responses.

PubMed ID: 24075985

DOI: 10.1016/j.celrep.2013.08.025

PubMed ID: 24698160

Title: Distinct biochemical properties of human serine hydroxymethyltransferase compared with the Plasmodium enzyme: implications for selective inhibition.

PubMed ID: 24698160

DOI: 10.1111/febs.12803

PubMed ID: 24275569

Title: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.

PubMed ID: 24275569

DOI: 10.1016/j.jprot.2013.11.014

PubMed ID: 25619277

Title: How pyridoxal 5'-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state.

PubMed ID: 25619277

DOI: 10.1111/febs.13211

PubMed ID: 9753690

Title: The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy.

PubMed ID: 9753690

DOI: 10.1016/s0969-2126(98)00112-9

Sequence Information:

  • Length: 483
  • Mass: 53083
  • Checksum: 6CDD6CA06D017C19
  • Sequence:
    • MTMPVNGAHK DADLWSSHDK MLAQPLKDSD VEVYNIIKKE SNRQRVGLEL IASENFASRA 
VLEALGSCLN NKYSEGYPGQ RYYGGTEFID ELETLCQKRA LQAYKLDPQC WGVNVQPYSG 
SPANFAVYTA LVEPHGRIMG LDLPDGGHLT HGFMTDKKKI SATSIFFESM PYKVNPDTGY 
INYDQLEENA RLFHPKLIIA GTSCYSRNLE YARLRKIADE NGAYLMADMA HISGLVAAGV 
VPSPFEHCHV VTTTTHKTLR GCRAGMIFYR KGVKSVDPKT GKEILYNLES LINSAVFPGL 
QGGPHNHAIA GVAVALKQAM TLEFKVYQHQ VVANCRALSE ALTELGYKIV TGGSDNHLIL 
VDLRSKGTDG GRAEKVLEAC SIACNKNTCP GDRSALRPSG LRLGTPALTS RGLLEKDFQK 
VAHFIHRGIE LTLQIQSDTG VRATLKEFKE RLAGDKYQAA VQALREEVES FASLFPLPGL 
PDF

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.