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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 2.1.2.1 4 61
  • 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 Glycine, serine and threonine metabolism and Metabolism. 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F018376 1.2 Ensembl ENCODE 39.9 -14.1 -14138 1.8 GTF2F1 TBP CTCF MXI1 KLF17 MAX CEBPG RAD21 RFX5 ZKSCAN1 SHMT1 MIEF2 EVPLL GC17M018777 PIR37765
GH17F018361 0.5 ENCODE 39 +0.5 497 2.2 HDGF ATF1 MLX ARID4B SIN3A DMAP1 YY1 GLIS2 FOS SP3 SHMT1 MIR6778 GC17M018331
GH17F018369 0.4 ENCODE 37.3 -5.6 -5639 0.2 ARID1B GATA3 FOS SHMT1 PIRC91 MIR6778
GH17F018267 0.8 Ensembl ENCODE 36.1 +95.1 95111 1.2 ZNF263 MAZ SP2 ZIC2 SSRP1 ZFHX2 PATZ1 IKZF1 EGR2 ZBTB20 SHMT1 TOP3A RPL21P121 SMCR8 LLGL1 MIR6778 MYO15A DRG2 ENSG00000260647 GC17M018275
GH17F018388 0.2 Ensembl 35.1 -25.3 -25338 1.0 POLR2A SHMT1 MIEF2 FAM106A ENSG00000264177 ENSG00000267441
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

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
ENSR00001342194 463 1801 ATF1 MLX ARID4B SIN3A DMAP1 YY1 GLIS2 FOS SP3 NFYC

Genomic Location for SHMT1 Gene

Chromosome:
17
Start:
18,327,860 bp from pter
End:
18,363,563 bp from pter
Size:
35,704 bases
Orientation:
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:
    P34896-GLYC_HUMAN
    Recommended name:
    Serine hydroxymethyltransferase, cytosolic
    Protein Accession:
    P34896
    Secondary Accessions:
    • B4DPM9
    • D3DXD0
    • Q96HY0
    • Q9UMD1
    • Q9UMD2

    Protein attributes for SHMT1 Gene

    Size:
    483 amino acids
    Molecular mass:
    53083 Da
    Cofactor:
    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).
    • 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).
    Miscellaneous:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for SHMT1 Gene

Selected DME Specific Peptides for SHMT1 Gene

P34896:
  • KVAHFIHRGIELTLQIQ
  • TGYINYDQLEENA
  • LIASENF
  • LVDLRSK
  • LQGGPHNH
  • GGHLTHG
  • NKNTCPGD
  • NSAVFPG
  • ANFAVYTA
  • TTHKTLRG
  • LCQKRAL
  • TTTTHKTL
  • AVALKQA
  • RYYGGTE
  • VTTTTHK
  • AVLEALGS
  • IAGVAVALK
  • NKYSEGYPG
  • PKLIIAG
  • SGSPANF
  • SGLVAAGV
  • YKVNPDTGYI
  • NVQPYSGS
  • DMAHISGLV
  • LFPLPGLP
  • IFYRKGV
  • TDKKKISA
  • LMADMAH

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

P34896

UniProtKB/Swiss-Prot:

GLYC_HUMAN :
  • Belongs to the SHMT family.
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:0004372 glycine hydroxymethyltransferase activity TAS --
GO:0004843 thiol-dependent ubiquitin-specific protease activity IEA --
GO:0005515 protein binding IPI 25416956
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

  • Taconic Biosciences Mouse Models for SHMT1

miRNA for SHMT1 Gene

miRTarBase miRNAs that target SHMT1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SHMT1

Flow Cytometry 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

COMPARTMENTS
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

Gene Ontology (GO) - Cellular Components for SHMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IDA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 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

(23) 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 226
Tetrahydrofolic acid Approved Nutra Target, cofactor 0
Bevacizumab Approved, Investigational Pharma VEGF antagonist, Therapeutic Antibodies, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors 1968
Capecitabine Approved, Investigational Pharma RNA processing inhibitor and thymidylate synthase inhibitor, F-pyrimidines 1296

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5,10-Methylenetetrahydromethanopterin
5,10-Methylene-THF
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-Methylene-THF
31690-11-6
5,6,7,8-Tetrahydromethanopterin
genes like me logo Genes that share compounds with SHMT1: view

Transcripts for SHMT1 Gene

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SHMT1

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
SHMT1
ECgene alternative splicing isoforms for
SHMT1

Expression for SHMT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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:

SHMT1

SOURCE GeneReport for Unigene cluster for SHMT1 Gene:

Hs.513987
genes like me logo Genes that share expression patterns with SHMT1: view

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
chimpanzee
(Pan troglodytes)
Mammalia SHMT1 34 35
  • 99.59 (n)
dog
(Canis familiaris)
Mammalia SHMT1 34 35
  • 88.13 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SHMT1 35
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SHMT1 34 35
  • 85.44 (n)
mouse
(Mus musculus)
Mammalia Shmt1 34 16 35
  • 85.22 (n)
rat
(Rattus norvegicus)
Mammalia Shmt1 34
  • 84.31 (n)
oppossum
(Monodelphis domestica)
Mammalia SHMT1 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves SHMT1 34 35
  • 74.67 (n)
lizard
(Anolis carolinensis)
Reptilia SHMT1 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia shmt1 34
  • 72.38 (n)
Str.15846 34
African clawed frog
(Xenopus laevis)
Amphibia shmt1-prov 34
zebrafish
(Danio rerio)
Actinopterygii shmt1 34 35
  • 73.06 (n)
zgc66171 34
fruit fly
(Drosophila melanogaster)
Insecta CG3011 36 34 35
  • 61.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001065 34
  • 60.95 (n)
worm
(Caenorhabditis elegans)
Secernentea mel-32 36 34 35
  • 60.73 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR215C 34
  • 59.04 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08921g 34
  • 56.88 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SHM2 34 35
  • 56.57 (n)
SHM1 35
  • 52 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons SHM2 34
  • 58.15 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8061 34
barley
(Hordeum vulgare)
Liliopsida Hv.2416 34
corn
(Zea mays)
Liliopsida Zm.3136 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 66 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU02274 34
  • 59.99 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC24C9.12c 34
  • 57.1 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4793 34
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

ENSEMBL:
Gene Tree for SHMT1 (if available)
TreeFam:
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.org 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 Uncertain significance 18,328,782(+) GAAGA(A/G)AGAGG reference, missense
rs10163522 -- 18,329,724(+) GCCCT(A/G)ACCTC intron-variant
rs10560620 -- 18,357,294(+) ACCTC(-/A)AAAAA intron-variant, upstream-variant-2KB
rs10655994 -- 18,344,577(+) AAAAA(-/A/AA/AAA/GA)GCCTG intron-variant
rs11078415 -- 18,352,184(+) gctat(C/T)gccca intron-variant

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

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

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)
SHMT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHMT1

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

Disorders for SHMT1 Gene

MalaCards: The human disease database

(8) 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
  • 17p11.2 microdeletion syndrome
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
lacrimal gland adenoid cystic carcinoma
  • adenoid cystic carcinoma 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)
SHMT1
Human Genome Epidemiology (HuGE) Navigator
SHMT1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SHMT1
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 22 64
  2. No association between cSHMT genotypes and the risk of breast cancer in the Nurses' Health Study. (PMID: 19707223) Bentley A.R. … Cassano P.A. (Eur J Clin Nutr 2010) 3 22 46 64
  3. Methotrexate in pediatric osteosarcoma: response and toxicity in relation to genetic polymorphisms and dihydrofolate reductase and reduced folate carrier 1 expression. (PMID: 19159907) PatiA+o-GarcA-a A. … SierrasesA_maga L. (J. Pediatr. 2009) 3 22 46 64
  4. Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan. (PMID: 17896178) Cheng C.W. … Shen C.Y. (Breast Cancer Res. Treat. 2008) 3 22 46 64
  5. A high frequency of the MTHFR 677C>T polymorphism in Scottish women with epilepsy: possible role in pathogenesis. (PMID: 17904392) Dean J.C. … Little J. (Seizure 2008) 3 22 46 64

Products for SHMT1 Gene

Sources for SHMT1 Gene

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