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Aliases for SHMT1 Gene

Aliases for SHMT1 Gene

  • Serine Hydroxymethyltransferase 1 (Soluble) 2 3
  • Cytoplasmic Serine Hydroxymethyltransferase 2 3
  • Glycine Hydroxymethyltransferase 3 4
  • Serine Methylase 3 4
  • EC 4 63
  • SHMT 3 4
  • Serine Hydroxymethyltransferase, Cytosolic 3
  • 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 (Soluble)) is a Protein Coding gene. Diseases associated with SHMT1 include adult acute lymphocytic leukemia and pediatric osteosarcoma. Among its related pathways are Disease and Metabolism. GO annotations related to this gene include protein homodimerization activity and amino acid binding. An important paralog of this gene is SHMT2.

UniProtKB/Swiss-Prot for SHMT1 Gene

  • Interconversion of serine and glycine

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

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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
    • 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 Lys72, Lys98, Lys105, Lys375, Lys386, Lys416, Lys420, and Lys456
  • Modification sites at PhosphoSitePlus

Other Protein References for SHMT1 Gene

Antibody Products

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

Domains for SHMT1 Gene

Graphical View of Domain Structure for InterPro Entry



  • P34896
  • 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 CatalyticActivity:
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
UniProtKB/Swiss-Prot Function:
Interconversion of serine and glycine

Enzyme Numbers (IUBMB) for SHMT1 Gene

Gene Ontology (GO) - Molecular Function for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004372 glycine hydroxymethyltransferase activity TAS --
GO:0005515 protein binding IPI 25416956
GO:0008242 omega peptidase activity --
GO:0008732 L-allo-threonine aldolase activity IEA --
GO:0016597 amino acid 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

miRNA for SHMT1 Gene

miRTarBase miRNAs that target SHMT1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SHMT1

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting 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
nucleus 4
chloroplast 2
mitochondrion 2
extracellular 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SHMT1: view

Pathways for SHMT1 Gene

SuperPathways for SHMT1 Gene

Superpath Contained pathways
1 Defective BTD causes biotidinase deficiency
2 One carbon pool by folate
3 Glycine, serine and threonine metabolism
4 folate polyglutamylation
5 Metabolism
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:0006508 proteolysis --
GO:0006544 glycine metabolic process --
GO:0006545 glycine biosynthetic process --
GO:0006563 L-serine metabolic process --
GO:0006565 L-serine catabolic process IDA 17482557
genes like me logo Genes that share ontologies with SHMT1: view

Compounds for SHMT1 Gene

(6) HMDB Compounds for SHMT1 Gene

Compound Synonyms Cas Number PubMed IDs
  • 5,10-methylene-THF
  • 2-Aminoacetate
  • (-)-Serine
Pyridoxal 5'-phosphate
  • Apolon B6
Tetrahydrofolic acid
  • (6S)-Tetrahydrofolate

(7) Drugbank Compounds for SHMT1 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
5-Hydroxymethylene-6-Hydrofolic Acid
  • 2-Aminoacetic acid
56-40-6 target
  • L-Mimosine
500-44-7 target inhibitor
Pyridoxal Phosphate
  • Codecarboxylase
54-47-7 target cofactor

(18) Novoseek inferred chemical compound relationships for SHMT1 Gene

Compound -log(P) Hits PubMed IDs
tetrahydrofolate 87.3 5
thymidylate 84 24
serine 78.8 76
folate 78.6 17
pyridoxal 5-phosphate 75.3 9

(5) PharmGKB related drug/compound annotations for SHMT1 Gene

Drug/compound Annotation
bevacizumab CA
fluorouracil CA
irinotecan CA
leucovorin CA
methotrexate CA
genes like me logo Genes that share compounds with SHMT1: view

Transcripts for SHMT1 Gene

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SHMT1

Primer Products

Flow Cytometry Products

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 expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Liver (15.6) and Kidney - Cortex (6.6).

Protein differential expression in normal tissues for SHMT1 Gene

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

Integrated Proteomics: protein expression 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 expressions with SHMT1: view

Expression partners for SHMT1 Gene

In Situ Assay Products

No data available for 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

Selected 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 MAF
rs3783 -- 18,328,703(+) GGCAG(C/G)CAGCT utr-variant-3-prime
rs593297 -- 18,365,454(+) caggc(A/G)tgagt upstream-variant-2KB
rs599147 -- 18,354,889(-) gtatt(A/T)ttttt intron-variant
rs638318 -- 18,354,836(-) gatct(C/T)gatct intron-variant
rs638416 -- 18,363,661(-) CGCCC(C/G)GGAGA upstream-variant-2KB

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

Relevant External Links for SHMT1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

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

Disorders for SHMT1 Gene

(8) Novoseek inferred disease relationships for SHMT1 Gene

Disease -log(P) Hits PubMed IDs
adult acute lymphocytic leukemia 77.4 1
neural tube defects 54.6 1
cancer 15 7
breast cancer 13.7 11
colorectal cancer 13.3 2

Relevant External Links for SHMT1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SHMT1: view

No data available for OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES 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
  2. 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 48
  3. Isolation and characterisation of human genomic sequences encoding cytosolic serine hydroxymethyltransferase. (PMID: 9056951) Chave K.J. … Sanders P.G. (Biochem. Soc. Trans. 1997) 3 4 23
  4. The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. (PMID: 9753690) Renwick S.B. … Baumann U. (Structure 1998) 3 4 23
  5. Associations between polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and susceptibility to malignant lymphoma. (PMID: 12604405) Hishida A. … Tajima K. (Haematologica 2003) 3 23 48

Products for SHMT1 Gene

Sources for SHMT1 Gene

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