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Aliases for SHMT1 Gene

Aliases for SHMT1 Gene

  • Serine Hydroxymethyltransferase 1 2 3
  • Serine Hydroxymethyltransferase 1 (Soluble) 2 3 5
  • Cytoplasmic Serine Hydroxymethyltransferase 2 3
  • Glycine Hydroxymethyltransferase 3 4
  • Serine Methylase 3 4
  • EC 4 63
  • SHMT 3 4
  • 14 KDa Protein 2
  • CSHMT 3

External Ids for SHMT1 Gene

Previous GeneCards Identifiers for SHMT1 Gene

  • GC17M018476
  • GC17M019823
  • GC17M018174
  • GC17M018431
  • GC17M018171
  • GC17M017984
  • GC17M018231

Summaries for SHMT1 Gene

Entrez Gene Summary for SHMT1 Gene

  • This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

GeneCards Summary for SHMT1 Gene

SHMT1 (Serine Hydroxymethyltransferase 1) is a Protein Coding gene. Diseases associated with SHMT1 include Adult Acute Lymphocytic Leukemia and Smith-Magenis Syndrome. Among its related pathways are Glucose / Energy Metabolism and Valine, leucine and isoleucine degradation. GO annotations related to this gene include protein homodimerization activity and pyridoxal phosphate binding. An important paralog of this gene is SHMT2.

UniProtKB/Swiss-Prot for SHMT1 Gene

  • Interconversion of serine and glycine (PubMed:8505317, PubMed:24698160).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SHMT1 Gene

Genomics for SHMT1 Gene

Regulatory Elements for SHMT1 Gene

Enhancers for SHMT1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SHMT1 on UCSC Golden Path with GeneCards custom track

Promoters for SHMT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SHMT1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SHMT1 Gene

18,327,860 bp from pter
18,363,563 bp from pter
35,704 bases
Minus strand

Genomic View for SHMT1 Gene

Genes around SHMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHMT1 Gene

Proteins for SHMT1 Gene

  • Protein details for SHMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Serine hydroxymethyltransferase, cytosolic
    Protein Accession:
    Secondary Accessions:
    • B4DPM9
    • D3DXD0
    • Q96HY0
    • Q9UMD1
    • Q9UMD2

    Protein attributes for SHMT1 Gene

    483 amino acids
    Molecular mass:
    53083 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homotetramer (PubMed:24698160, PubMed:25619277, PubMed:9753690). Identified in complex with FAM175B and the other subunits of the BRISC complex, at least composed of FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and BABAM1/NBA1 (PubMed:24075985).
    • In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.

    Three dimensional structures from OCA and Proteopedia for SHMT1 Gene

    Alternative splice isoforms for SHMT1 Gene


neXtProt entry for SHMT1 Gene

Proteomics data for SHMT1 Gene at MOPED

Post-translational modifications for SHMT1 Gene

  • Ubiquitination at Lys 72, Lys 98, Lys 105, Lys 375, Lys 386, Lys 416, Lys 420, and Lys 456
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SHMT1 (SHMT1)

Domains & Families for SHMT1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SHMT family.
  • Belongs to the SHMT family.
genes like me logo Genes that share domains with SHMT1: view

No data available for Gene Families for SHMT1 Gene

Function for SHMT1 Gene

Molecular function for SHMT1 Gene

GENATLAS Biochemistry:
serine hydroxy-methyltransferase,cytosolic,with several alternatively spliced isoforms,catalyzing serine synthesis,"one-carbone" metabolism,constantly deleted in Smith-Magenis syndrome,putative regulator of cell growth and proliferation
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.18 mM for L-serine {ECO:0000269 PubMed:24698160}; KM=5.2 uM for tetrahydrofolate {ECO:0000269 PubMed:24698160};
UniProtKB/Swiss-Prot CatalyticActivity:
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by tetrahydrofolate concentrations above 40 uM.
UniProtKB/Swiss-Prot Function:
Interconversion of serine and glycine (PubMed:8505317, PubMed:24698160).

Enzyme Numbers (IUBMB) for SHMT1 Gene

Gene Ontology (GO) - Molecular Function for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008242 omega peptidase activity IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with SHMT1: view
genes like me logo Genes that share phenotypes with SHMT1: view

Animal Models for SHMT1 Gene

MGI Knock Outs for SHMT1:

Animal Model Products

  • Taconic Biosciences Mouse Models for SHMT1

miRNA for SHMT1 Gene

miRTarBase miRNAs that target SHMT1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHMT1 Gene

Localization for SHMT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHMT1 Gene


Subcellular locations from

Jensen Localization Image for SHMT1 Gene COMPARTMENTS Subcellular localization image for SHMT1 gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5
mitochondrion 4
chloroplast 1
peroxisome 1
plasma membrane 1

No data available for Gene Ontology (GO) - Cellular Components for SHMT1 Gene

Pathways & Interactions for SHMT1 Gene

genes like me logo Genes that share pathways with SHMT1: view

UniProtKB/Swiss-Prot P34896-GLYC_HUMAN

  • Pathway: One-carbon metabolism; tetrahydrofolate interconversion.

Gene Ontology (GO) - Biological Process for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006544 glycine metabolic process IEA,IDA 24698160
GO:0006545 glycine biosynthetic process IEA --
GO:0006766 vitamin metabolic process TAS --
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with SHMT1: view

No data available for SIGNOR curated interactions for SHMT1 Gene

Drugs & Compounds for SHMT1 Gene

(22) Drugs for SHMT1 Gene - From: DrugBank, PharmGKB, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Mimosine Approved Pharma Target, inhibitor 0
Glycine Approved Nutra Full agonist, Agonist, Target, Target, Target Endogenous potentiator, co-transmitter 197
Tetrahydrofolic acid Approved Nutra Target, Target, Target, cofactor 0
Bevacizumab Approved, Investigational Pharma VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 1910
Capecitabine Approved, Investigational Pharma RNA processing inhibitor and thymidylate synthase inhibitor, F-pyrimidines 1239

(13) Additional Compounds for SHMT1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-Methylene-THF
  • Dihydrogen oxide
  • Steam
genes like me logo Genes that share compounds with SHMT1: view

Transcripts for SHMT1 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for SHMT1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - -
SP2: - - - -
SP3: - -
SP4: - -
SP5: -

Relevant External Links for SHMT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SHMT1 Gene

mRNA expression in normal human tissues for SHMT1 Gene

mRNA differential expression in normal tissues according to GTEx for SHMT1 Gene

This gene is overexpressed in Liver (x15.6) and Kidney - Cortex (x6.6).

Protein differential expression in normal tissues from HIPED for SHMT1 Gene

This gene is overexpressed in Liver, secretome (29.6), Kidney (8.5), and Liver (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SHMT1 Gene

SOURCE GeneReport for Unigene cluster for SHMT1 Gene Hs.513987

genes like me logo Genes that share expression patterns with SHMT1: view

Protein tissue co-expression partners for SHMT1 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for SHMT1 Gene

Orthologs for SHMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SHMT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia SHMT1 35
  • 85.44 (n)
  • 90.06 (a)
SHMT1 36
  • 90 (a)
(Canis familiaris)
Mammalia SHMT1 35
  • 88.13 (n)
  • 91.1 (a)
SHMT1 36
  • 91 (a)
(Mus musculus)
Mammalia Shmt1 35
  • 85.22 (n)
  • 91.6 (a)
Shmt1 16
Shmt1 36
  • 91 (a)
(Pan troglodytes)
Mammalia SHMT1 35
  • 99.59 (n)
  • 99.79 (a)
SHMT1 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Shmt1 35
  • 84.31 (n)
  • 91.18 (a)
(Monodelphis domestica)
Mammalia SHMT1 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia SHMT1 36
  • 87 (a)
(Gallus gallus)
Aves SHMT1 35
  • 74.67 (n)
  • 81.68 (a)
SHMT1 36
  • 73 (a)
(Anolis carolinensis)
Reptilia SHMT1 36
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shmt1 35
  • 72.38 (n)
  • 80.75 (a)
Str.15846 35
African clawed frog
(Xenopus laevis)
Amphibia shmt1-prov 35
(Danio rerio)
Actinopterygii shmt1 35
  • 73.06 (n)
  • 80.38 (a)
zgc66171 35
shmt1 36
  • 79 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3011 37
  • 60 (a)
CG3011 35
  • 61.04 (n)
  • 60.39 (a)
CG3011 36
  • 52 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001065 35
  • 60.95 (n)
  • 66.38 (a)
(Caenorhabditis elegans)
Secernentea mel-32 37
  • 61 (a)
mel-32 35
  • 60.73 (n)
  • 61.8 (a)
mel-32 36
  • 57 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR215C 35
  • 59.04 (n)
  • 55.29 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08921g 35
  • 56.88 (n)
  • 55.51 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SHM2 35
  • 56.57 (n)
  • 55.84 (a)
SHM1 36
  • 52 (a)
SHM2 36
  • 55 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons SHM2 35
  • 58.15 (n)
  • 60.17 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8061 35
(Hordeum vulgare)
Liliopsida Hv.2416 35
(Zea mays)
Liliopsida Zm.3136 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4793 35
bread mold
(Neurospora crassa)
Ascomycetes NCU02274 35
  • 59.99 (n)
  • 58.62 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC24C9.12c 35
  • 57.1 (n)
  • 57.83 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 66 (a)
Species with no ortholog for SHMT1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SHMT1 Gene

Gene Tree for SHMT1 (if available)
Gene Tree for SHMT1 (if available)

Paralogs for SHMT1 Gene

Paralogs for SHMT1 Gene

(3) SIMAP similar genes for SHMT1 Gene using alignment to 5 proteins: Pseudogenes for SHMT1 Gene

genes like me logo Genes that share paralogs with SHMT1: view

Variants for SHMT1 Gene

Sequence variations from dbSNP and Humsavar for SHMT1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1979277 - 18,328,782(+) GAAGA(A/G)AGAGG reference, missense
rs7215148 - 18,333,202(+) GGCCT(C/G)AGACA intron-variant, reference, missense
rs3783 -- 18,328,703(+) GGCAG(C/G)CAGCT utr-variant-3-prime
rs593297 -- 18,365,454(+) caggc(A/G/T)tgagt upstream-variant-2KB
rs599147 -- 18,354,889(-) gtatt(A/T)ttttt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SHMT1 Gene

Variant ID Type Subtype PubMed ID
nsv155 OTHER Inversion 15895083
nsv499114 OTHER Inversion 21111241
nsv833386 CNV Gain 17160897
nsv833387 CNV Loss 17160897
nsv428333 CNV Gain 18775914
esv1004827 CNV Deletion 20482838
nsv509653 CNV Insertion 20534489
dgv932e1 CNV Complex 17122850
nsv827913 CNV Gain 20364138
nsv1998 CNV Insertion 18451855

Variation tolerance for SHMT1 Gene

Residual Variation Intolerance Score: 39.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.06; 75.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SHMT1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHMT1 Gene

Disorders for SHMT1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SHMT1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
adult acute lymphocytic leukemia
  • adult acute lymphoid leukemia
smith-magenis syndrome
  • smith magenis syndrome
lacrimal gland carcinoma
  • carcinoma of the lacrimal gland
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
lacrimal system cancer
  • lacrimal system neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search SHMT1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SHMT1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SHMT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHMT1 Gene

Publications for SHMT1 Gene

  1. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PMID: 8505317) Garrow T.A. … Shane B. (J. Biol. Chem. 1993) 2 3 4 23 67
  2. Mimosine attenuates serine hydroxymethyltransferase transcription by chelating zinc. Implications for inhibition of DNA replication. (PMID: 15531579) Perry C. … Stover P.J. (J. Biol. Chem. 2005) 3 23 25 26
  3. Molecular cloning and biochemical characterization of Leishmania donovani serine hydroxymethyltransferase. (PMID: 17142057) Vatsyayan R. … Roy U. (Protein Expr. Purif. 2007) 23 25 26
  4. In silico experimentation with a model of hepatic mitochondrial folate metabolism. (PMID: 17150100) Nijhout H.F. … Ulrich C.M. (Theor Biol Med Model 2006) 23 25 26
  5. Is mutated serine hydroxymethyltransferase (SHMT) involved in the etiology of neural tube defects? (PMID: 11386852) Heil S.G. … Blom H.J. (Mol. Genet. Metab. 2001) 3 23 25

Products for SHMT1 Gene

Sources for SHMT1 Gene