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Aliases for SHMT1 Gene

Aliases for SHMT1 Gene

  • Serine Hydroxymethyltransferase 1 2 3 5
  • Cytoplasmic Serine Hydroxymethyltransferase 2 3
  • Serine Hydroxymethyltransferase 1 (Soluble) 2 3
  • Glycine Hydroxymethyltransferase 3 4
  • Serine Methylase 3 4
  • EC 4 56
  • 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) is a Protein Coding gene. Diseases associated with SHMT1 include Adult Acute Lymphocytic Leukemia and Smith-Magenis Syndrome. Among its related pathways are serine and glycine biosynthesis and One carbon pool by folate. Gene Ontology (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).

Additional gene information for SHMT1 Gene

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

Genomics for SHMT1 Gene

GeneHancer (GH) Regulatory Elements for SHMT1 Gene

Promoters and enhancers for SHMT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I018361 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 589 +0.5 496 2.2 HDGF CLOCK MLX ARID4B SIN3A DMAP1 YY1 ZNF143 FOS SP3 SHMT1 SMCR8 DRG2 FLII ENSG00000262202 TOP3A MIR6778
GH17I018313 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 28.2 +47.8 47813 5.2 HDGF PKNOX1 CLOCK ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 E2F8 SMCR8 TOP3A DRG2 FLII SHMT1 FOXO3B ENSG00000262202 FAM106A ENSG00000264885 TVP23B
GH17I018256 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 28 +104.0 104037 6.3 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF207 MIEF2 FLII SHMT1 FAM106A LLGL1 SMCR8 FOXO3B ENSG00000264885 ENSG00000262202 DRG2
GH17I018377 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 39.9 -14.2 -14246 1.2 CTCF MXI1 FOXA2 TAF1 KLF17 MAX CEBPG RAD21 RFX5 YY1 EVPLL SHMT1 MIEF2 GC17M018912 PIR37765 PIRC91
GH17I018223 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 19.5 +138.3 138306 2.8 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF48 ETS1 GLIS2 LLGL1 PIR34011 SMCR8 TOP3A SHMT1 FAM106A MIEF2 ENSG00000273018 ENSG00000262202 DRG2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SHMT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SHMT1 gene promoter:

Genomic Locations for SHMT1 Gene

Genomic Locations for SHMT1 Gene
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 ABRAXAS2 and the other subunits of the BRISC complex, at least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 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

Selected DME Specific Peptides for SHMT1 Gene


Post-translational modifications for SHMT1 Gene

  • Ubiquitination at isoforms=2, 372, posLast=9898, isoforms=2, 3105, posLast=375375, isoforms=2, 3, 4386, isoforms=2, 3, 4416, isoforms=2, 3, 4420, and isoforms=2, 3, 4456

Domains & Families for SHMT1 Gene

Gene Families for SHMT1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • FDA approved drug targets
  • Plasma proteins
  • Predicted intracellular proteins

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

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

Phenotypes From GWAS Catalog for SHMT1 Gene

Gene Ontology (GO) - Molecular Function for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000900 translation repressor activity, nucleic acid binding IDA 10995219
GO:0003824 catalytic activity IEA --
GO:0004372 glycine hydroxymethyltransferase activity IDA,EXP 8505317
GO:0004843 thiol-dependent ubiquitin-specific protease activity IEA --
GO:0005515 protein binding IPI 25416956
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

CRISPR Products

miRNA for SHMT1 Gene

miRTarBase miRNAs that target SHMT1

Inhibitory RNA Products

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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHMT1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 3
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA,HDA 19056867
genes like me logo Genes that share ontologies with SHMT1: view

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:0006231 dTMP biosynthetic process IEA --
GO:0006544 glycine metabolic process IDA 24698160
GO:0006545 glycine biosynthetic process IEA --
GO:0006563 L-serine metabolic process IDA 24698160
GO:0006565 L-serine catabolic process IDA 17482557
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, Vet_approved Nutra Full agonist, Agonist, Target 254
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Bevacizumab Approved, Investigational Pharma VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 2087
Fluorouracil Approved Pharma RNA processing inhibitor and thymidylate synthase inhibitor 1970

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

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

Transcripts for SHMT1 Gene

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for SHMT1 Gene

Protein tissue co-expression partners for SHMT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SHMT1 Gene:


SOURCE GeneReport for Unigene cluster for SHMT1 Gene:


Evidence on tissue expression from TISSUES for SHMT1 Gene

  • Liver(4.7)
  • Bone marrow(4.1)
  • Nervous system(3.8)
  • Kidney(3.7)
  • Blood(2.3)
genes like me logo Genes that share expression patterns with SHMT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia SHMT1 33 34
  • 99.59 (n)
(Canis familiaris)
Mammalia SHMT1 33 34
  • 88.13 (n)
(Ornithorhynchus anatinus)
Mammalia SHMT1 34
  • 87 (a)
(Bos Taurus)
Mammalia SHMT1 33 34
  • 85.44 (n)
(Mus musculus)
Mammalia Shmt1 33 16 34
  • 85.22 (n)
(Rattus norvegicus)
Mammalia Shmt1 33
  • 84.31 (n)
(Monodelphis domestica)
Mammalia SHMT1 34
  • 84 (a)
(Gallus gallus)
Aves SHMT1 33 34
  • 74.67 (n)
(Anolis carolinensis)
Reptilia SHMT1 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shmt1 33
  • 72.38 (n)
Str.15846 33
African clawed frog
(Xenopus laevis)
Amphibia shmt1-prov 33
(Danio rerio)
Actinopterygii shmt1 33 34
  • 73.06 (n)
zgc66171 33
fruit fly
(Drosophila melanogaster)
Insecta CG3011 35 33 34
  • 61.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001065 33
  • 60.95 (n)
(Caenorhabditis elegans)
Secernentea mel-32 35 33 34
  • 60.73 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR215C 33
  • 59.04 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08921g 33
  • 56.88 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SHM2 33 34
  • 56.57 (n)
SHM1 34
  • 52 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons SHM2 33
  • 58.15 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8061 33
(Hordeum vulgare)
Liliopsida Hv.2416 33
(Zea mays)
Liliopsida Zm.3136 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 66 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU02274 33
  • 59.99 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC24C9.12c 33
  • 57.1 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4793 33
Species where no ortholog for SHMT1 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1979277 uncertain-significance, Gastrointestinal stromal tumor 18,328,782(-) G/A coding_sequence_variant, missense_variant
rs1000004147 -- 18,361,372(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000260186 -- 18,339,637(-) T/G intron_variant
rs1000321158 -- 18,346,757(-) G/A intron_variant
rs1000330832 -- 18,346,991(-) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
nsv833387 CNV loss 17160897
nsv833386 CNV gain 17160897
nsv827913 CNV gain 20364138
nsv509653 CNV insertion 20534489
nsv499114 OTHER inversion 21111241
nsv481238 CNV novel sequence insertion 20440878
nsv428333 CNV gain 18775914
nsv1998 CNV insertion 18451855
nsv155 OTHER inversion 15895083
nsv1129384 OTHER inversion 24896259
esv3640147 CNV loss 21293372
esv2758677 CNV gain+loss 17122850
esv1004827 CNV deletion 20482838

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)

Additional Variant Information for SHMT1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for SHMT1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
adult acute lymphocytic leukemia
  • adult acute lymphoid leukemia
smith-magenis syndrome
  • sms
potocki-luspski syndrome
  • 17p11.2 microduplication syndrome
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

Additional Disease Information for SHMT1

Genetic Association Database
Human Genome Epidemiology 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 TA … Shane B (The Journal of biological chemistry 1993) 2 3 4 22 58
  2. No association between cSHMT genotypes and the risk of breast cancer in the Nurses' Health Study. (PMID: 19707223) Bentley AR … Cassano PA (European journal of clinical nutrition 2010) 3 22 44 58
  3. Methotrexate in pediatric osteosarcoma: response and toxicity in relation to genetic polymorphisms and dihydrofolate reductase and reduced folate carrier 1 expression. (PMID: 19159907) Patiño-García A … Sierrasesúmaga L (The Journal of pediatrics 2009) 3 22 44 58
  4. A high frequency of the MTHFR 677C>T polymorphism in Scottish women with epilepsy: possible role in pathogenesis. (PMID: 17904392) Dean JC … Little J (Seizure 2008) 3 22 44 58
  5. Cardiac autonomic dysfunction: effects from particulate air pollution and protection by dietary methyl nutrients and metabolic polymorphisms. (PMID: 18378616) Baccarelli A … Schwartz J (Circulation 2008) 3 22 44 58

Products for SHMT1 Gene

Sources for SHMT1 Gene

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