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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SHMT1 Gene

protein-coding   GIFtS: 66
GCID: GC17M018231

Serine Hydroxymethyltransferase 1 (Soluble)

Microbiology & Infectious Diseases Congress
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Serine Hydroxymethyltransferase 1 (Soluble)1 2     EC 2.1.2.13 8
Cytoplasmic Serine Hydroxymethyltransferase1 2     14 KDa Protein1
Glycine Hydroxymethyltransferase2 3     CSHMT2
Serine Methylase2 3     Serine Hydroxymethyltransferase, Cytosolic2
SHMT2 3     

External Ids:    HGNC: 108501   Entrez Gene: 64702   Ensembl: ENSG000001769747   OMIM: 1821445   UniProtKB: P348963   

Export aliases for SHMT1 gene to outside databases

Previous GC identifers: GC17M018476 GC17M019823 GC17M018174 GC17M018431 GC17M018171 GC17M017984


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and among its related super-pathways are glycine biosynthesis I and One carbon pool by folate. GO annotations related to this gene include amino acid binding and protein homodimerization activity. An important paralog of this gene is SHMT2.

UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
Function: Interconversion of serine and glycine




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NT_010718.16  NC_018928.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SHMT1 gene promoter:
         AhR   CHOP-10   CBF-B   CBF-A   NF-YA   c-Myb   CP1A   NF-Y   CBF(2)   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SHMT1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SHMT1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SHMT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

SHMT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHMT1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M018231:  view genomic region     (about GC identifiers)

Start:
18,231,187 bp from pter      End:
18,266,856 bp from pter
Size:
35,670 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896 (See protein sequence)
Recommended Name: Serine hydroxymethyltransferase, cytosolic  
Size: 483 amino acids; 53083 Da
Cofactor: Pyridoxal phosphate
Subunit: Homotetramer
Subcellular location: Cytoplasm
Miscellaneous: In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one
1 PDB 3D structure from and Proteopedia for SHMT1:
1BJ4 (3D)    
Secondary accessions: D3DXD0 Q96HY0 Q9UMD1 Q9UMD2
Alternative splicing: 3 isoforms:  P34896-1   P34896-2   P34896-3   (Contains a N6-acetyllysine at position 271)

Explore the universe of human proteins at neXtProt for SHMT1: NX_P34896

Explore proteomics data for SHMT1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P34896

  • 4/28 DME Specific Peptides for SHMT1 (P34896) (see all 28)
     LCQKRAL  VTTTTHK  SGSPANF  LIASENF 

    SHMT1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SHMT1 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001268715.1  NP_004160.3  NP_683718.1  

    ENSEMBL proteins: 
     ENSP00000318868   ENSP00000462043   ENSP00000318805   ENSP00000462227   ENSP00000462041  
     ENSP00000345881   ENSP00000440089  
    Reactome Protein details: P34896
    Human Recombinant Protein Products for SHMT1: 
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    ProSpec Recombinant Protein for SHMT1
    Cloud-Clone Corp. Proteins for SHMT1 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005739mitochondrion IEA--
    GO:0005829cytosol TAS--

    SHMT1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    5 InterPro protein domains:
     IPR019798 Ser_HO-MeTrfase_PLP_BS
     IPR001085 Ser_HO-MeTrfase
     IPR015424 PyrdxlP-dep_Trfase
     IPR015421 PyrdxlP-dep_Trfase_major_sub1
     IPR015422 PyrdxlP-dep_Trfase_major_sub2

    Graphical View of Domain Structure for InterPro Entry P34896

    ProtoNet protein and cluster: P34896

    1 Blocks protein domain: IPB001085 Glycine hydroxymethyltransferase

    UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
    Similarity: Belongs to the SHMT family


    SHMT1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

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

         Genatlas biochemistry entry for SHMT1:
    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

         Enzyme Number (IUBMB): EC 2.1.2.11 2

         Gene Ontology (GO): 5/8 molecular function terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004372glycine hydroxymethyltransferase activity TAS--
    GO:0008168methyltransferase activity ----
    GO:0008242omega peptidase activity ----
    GO:0008732L-allo-threonine aldolase activity IEA--
    GO:0016597amino acid binding IEA--
         
    SHMT1 for ontologies           About GeneDecksing


    Phenotypes:
         4 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Shmt1):
     homeostasis/metabolism  liver/biliary system  mortality/aging  tumorigenesis 

    SHMT1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Shmt1tm1.1Stov for SHMT1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SHMT1 
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    SwitchGear 3'UTR luciferase reporter plasmidSHMT1 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SHMT1 About   (see all 14)                                                                                              See pathways by source

    SuperPathContained pathways About
    1glycine biosynthesis I
    glycine biosynthesis I0.67
    folate transformations I0.43
    superpathway of serine and glycine biosynthesis I0.67
    Metabolism of folate and pterines0.30
    folate polyglutamylation0.50
    2One Carbon Metabolism
    One carbon pool by folate0.53
    One Carbon Metabolism0.53
    3Metabolism
    Metabolism0.40
    Metabolic pathways0.40
    4Antimetabolite Pathway - Folate Cycle, Pharmacodynamics
    Antimetabolite Pathway - Folate Cycle, Pharmacodynamics0.87
    Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics0.36
    Methotrexate Pathway (Cancer Cell), Pharmacodynamics0.87
    5Metabolism of vitamins and cofactors
    Metabolism of water-soluble vitamins and cofactors1.00
    Metabolism of vitamins and cofactors1.00

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SHMT1
        Glucose / Energy Metabolism

    5/7 BioSystems Pathways for SHMT1 (see all 7)
        One Carbon Metabolism
    folate transformations I
    folate polyglutamylation
    Validated targets of C-MYC transcriptional activation
    glycine betaine degradation


    5/6        Reactome Pathways for SHMT1 (see all 6)
        Metabolism of folate and pterines
    Carnitine synthesis
    Metabolism
    Metabolism of vitamins and cofactors
    Metabolism of amino acids and derivatives

    3 PharmGKB Pathways for SHMT1
        Antimetabolite Pathway - Folate Cycle, Pharmacodynamics
    Methotrexate Pathway (Cancer Cell), Pharmacodynamics
    Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics

    5/7         Kegg Pathways  (Kegg details for SHMT1) (see all 7):
        Glycine, serine and threonine metabolism
    Cyanoamino acid metabolism
    Glyoxylate and dicarboxylate metabolism
    One carbon pool by folate
    Metabolic pathways

    UniProtKB/Swiss-Prot: GLYC_HUMAN, P34896
    Pathway: One-carbon metabolism; tetrahydrofolate interconversion


    SHMT1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SHMT1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/84 Interacting proteins for SHMT1 (P348963 ENSP000003188684) via UniProtKB, MINT, STRING, and/or I2D (see all 84)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    CSNK2BP678703, ENSP000003650254I2D: score=2 STRING: ENSP00000365025
    ENSG00000206406P678703I2D: score=2 
    ENSG00000224398P678703I2D: score=2 
    ENSG00000224774P678703I2D: score=2 
    ENSG00000228875P678703I2D: score=2 
    About this table

    Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006544glycine metabolic process ----
    GO:0006545glycine biosynthetic process ----
    GO:0006563L-serine metabolic process ----
    GO:0006565L-serine catabolic process IDA17482557
    GO:0006766vitamin metabolic process TAS--

    SHMT1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SHMT1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for SHMT1 (GLYC)

    6 HMDB Compounds for SHMT1    About this table
    CompoundSynonyms CAS #PubMed Ids
    5,10-Methylene-THF5,10-methylene-THF (see all 8)31690-11-6--
    Glycine2-Aminoacetate (see all 15)56-40-6--
    L-Serine(-)-Serine (see all 26)56-45-1--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--
    Tetrahydrofolic acid(6S)-Tetrahydrofolate (see all 10)135-16-0--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    7 DrugBank Compounds for SHMT1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor9305893 17139284 3143355 17016423 10592235 7526359
    Tetrahydrofolic acid5,6,7,8-tetrahydrofolate (see all 3)135-16-0targetcofactor12668769 11752472 10656824 11386852 10592235 10998057
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17664250 17150100 16876889 17142057 17355947
    MimosineL-Mimosine (see all 6)500-44-7targetinhibitor11936838 8576220 15531579 10766749
    5-Hydroxymethylene-6-Hydrofolic Acid-- --target--17139284 17016423 10592235
    N-Pyridoxyl-Glycine-5-Monophosphate-- --target--17139284 17016423 10592235
    Triglu-5-Formyl-Tetrahydrofolate-- --target--17139284 17016423 10592235

    10/18 Novoseek inferred chemical compound relationships for SHMT1 gene (see all 18)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tetrahydrofolate 87.3 9 11305908 (1), 11386852 (1), 12514178 (1), 9753690 (1) (see all 5)
    thymidylate 84 47 12161434 (3), 19513116 (3), 18067453 (3), 11516159 (1) (see all 18)
    serine 78.8 109 12161434 (4), 8527925 (3), 9675060 (3), 9753690 (3) (see all 53)
    folate 78.6 23 11386852 (2), 15122597 (1), 16536979 (1), 12161434 (1) (see all 16)
    pyridoxal 5-phosphate 75.3 21 17482557 (3), 12514178 (3), 8527925 (1), 9753690 (1) (see all 5)
    methionine 67.9 12 16536979 (1), 16410450 (1), 12161434 (1), 11986237 (1) (see all 8)
    mimosine 63.1 13 10766749 (4), 15531579 (4)
    deoxyribonucleotide 60.1 2 12161434 (1), 15531579 (1)
    dihydrofolate 55.4 8 19513116 (1), 18067453 (1), 11197757 (1), 17446168 (1)
    homocysteine 54.5 2 11386852 (1), 14656021 (1)

    1 PharmGKB related drug/compound annotation for SHMT1 gene    About this table
    Drug/compound PharmGKB Annotation
    methotrexateCA  

    Search CenterWatch for drugs/clinical trials and news about SHMT1 / GLYC

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for SHMT1 gene (3 alternative transcripts): 
    NM_001281786.1  NM_004169.4  NM_148918.2  

    Unigene Clusters for SHMT1:

    Serine hydroxymethyltransferase 1 (soluble)
    Hs.513987  [show with all ESTs], Hs.636044
    Unigene Representative Sequences: AK091498, Y14488
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000395684(uc002gsz.3) ENST00000316694(uc002gta.3 uc002gtb.3 uc010vxt.2)
    ENST00000580002 ENST00000354098 ENST00000582352(uc002gtc.1) ENST00000579558(uc010vxu.1)
    ENST00000582653 ENST00000395682 ENST00000583780 ENST00000352886 ENST00000539052

    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    Additional mRNA sequence: Y14488.1 

    17 DOTS entries:

    DT.418980  DT.100817283  DT.100817277  DT.100697358  DT.95237322  DT.97847235  DT.99938562  DT.95333677 
    DT.100817274  DT.421797  DT.92065961  DT.95237302  DT.100817271  DT.100834637  DT.120915249  DT.95237308 
    DT.100817278 

    24/453 AceView cDNA sequences (see all 453):

    BM471273 AI263578 CK819100 AA236270 BF477475 AI056643 BU731925 BX956375 
    CR599388 AI301173 BM792340 BQ880854 AA235011 AF017065 AA705609 AU143448 
    AI692771 AA578600 AV648103 AV648239 BX486945 BM704574 BM904280 AW195050 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SHMT1    About this scheme

    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:                          -                                                                                       


    ECgene alternative splicing isoforms for SHMT1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SHMT1 expression in normal human tissues (normalized intensities)      SHMT1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCAAAGGAGA
    SHMT1 Expression
    About this image


    SHMT1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/31 selected tissues (see all 31) fully expand
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             testis ; cells in seminiferus ducts   
     
     Tonsil (Hematopoietic System)    fully expand to see all 3 entries
             tonsil ; squamous epithelial cells   
     
     Uterus
             uterus, post-menopause ; glandular cells   
     
     Liver (Hepatobiliary System)    fully expand to see all 2 entries
             Hepatocytes Liver Lobule
             liver ; bile duct cells   

    See SHMT1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SHMT1

    SOURCE GeneReport for Unigene clusters: Hs.513987 Hs.636044
        SABiosciences Custom PCR Arrays for SHMT1
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for SHMT1 gene from 10/30 species (see all 30)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shmt11 , 5 serine hydroxymethyltransferase 1 (soluble)1, 5 85.22(n)1
    91.6(a)1
      11 (37.84 cM)5
    204251  NM_009171.21  NP_033197.21 
     607881045 
    chicken
    (Gallus gallus)
    Aves SHMT11 serine hydroxymethyltransferase 1 (soluble) 74.67(n)
    81.68(a)
      416520  XM_414824.3  XP_414824.3 
    lizard
    (Anolis carolinensis)
    Reptilia SHMT16
    Serine hydroxymethyltransferase
    82(a)
    1 ↔ 1
    GL343618.1(206498-225361)
    African clawed frog
    (Xenopus laevis)
    Amphibia shmt1-prov2 serine hydroxymethyltransferase 1 (soluble) 81.3(n)    BC042276.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc661712 similar to serine hydroxymethyl transferase 1 (soluble) 75.95(n)   394021  BC055527.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG30111 , 3 glycine hydroxymethyltransferase3
    CG30111
    60(a)3
    59.93(n)1
    60.43(a)1
      5C73
    315241  NM_132050.11  NP_572278.11 
    worm
    (Caenorhabditis elegans)
    Secernentea mel-321 , 3 Protein MEL-321 61(a)3
    60.87(n)1
    61.8(a)1
      III(6512024-6514577)3
    1759151  NM_171169.31  NP_741197.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SHM11 Shm1p 55.39(n)
    55.03(a)
      852565   NP_009822.4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SHM11 glycine hydroxymethyltransferase 59.17(n)
    60.26(a)
      829949  NM_119954.3  NP_195506.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g07384001 hypothetical protein 61.5(n)
    61.14(a)
      4334048  NM_001057746.1  NP_001051211.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SHMT1 gene
    SHMT22  
    3 SIMAP similar genes for SHMT1 using alignment to 5 protein entries:     GLYC_HUMAN (see all proteins):
    SHMT    SHMT2    DKFZp686P09201

    SHMT1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SHMT1
    PGOHUM00000243989


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/833 SNPs in SHMT1 are shown (see all 833)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1381949581,2
    C--18218863(+) GCCCTA/GGAGAT 2 -- ds50010--------
    rs802239401,2
    C,F--18218892(+) GGGGAG/AGGGTC 2 -- ds50012Minor allele frequency- A:0.04WA 120
    rs1900452701,2
    --18219039(+) CCTACA/GAGGTG 2 -- ds50010--------
    rs1491589131,2
    --18219135(+) TGCAGA/TGAAAA 2 -- ds50010--------
    rs1450722561,2
    --18219209(+) TTCCCA/GTCCCG 2 -- ds50010--------
    rs1831942591,2
    --18219243(+) ACCACA/GTGAGG 2 -- ds50010--------
    rs1380139791,2
    --18219294(+) CGTGTA/GTGATA 2 -- ds50010--------
    rs1426090601,2
    --18219569(+) GATTAC/TGGGAG 2 -- ut310--------
    rs1136408811,2
    C--18219594(+) CAGGTA/GGAGCA 2 -- ut310--------
    rs20454631,2
    C,H--18219683(+) ACTTTG/AAGCTA 2 -- ut316Minor allele frequency- A:0.00NS EA NA 424

    HapMap Linkage Disequilibrium report for SHMT1 (18231187 - 18266856 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for SHMT1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv1004827CNV Deletion20482838
    nsv1998CNV Insertion18451855
    nsv509653CNV Insertion20534489
    nsv833387CNV Loss17160897
    nsv428333CNV Gain18775914
    nsv827913CNV Gain20364138
    nsv833386CNV Gain17160897
    dgv932e1CNV Complex17122850
    nsv155OTHER Inversion15895083
    nsv499114OTHER Inversion21111241


    Human Gene Mutation Database (HGMD): SHMT1
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SHMT1
    DNA2.0 Custom Variant and Variant Library Synthesis for SHMT1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 182144    OMIM disorders: --

    20/47 diseases for SHMT1 (see all 47):    About MalaCards
    adult acute lymphocytic leukemia    pediatric osteosarcoma    smith magenis syndrome    childhood leukemia
    rift valley fever    acute lymphocytic leukemia    autonomic dysfunction    neural tube defects
    follicular lymphoma    patent ductus arteriosus    squamous cell carcinoma of the head and neck    abdominal aortic aneurysm
    hyperhomocysteinemia    spina bifida    aortic aneurysm    osteosarcoma
    non-hodgkin lymphoma    diffuse large b-cell lymphoma    vaccinia    migraine


    SHMT1 for disorders           About GeneDecksing

    8 Novoseek inferred disease relationships for SHMT1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    adult acute lymphocytic leukemia 77.4 1 12604405 (1)
    neural tube defects 54.6 1 11386852 (1)
    cancer 15 7 9753690 (2), 16049973 (2), 16410450 (1), 9757129 (1) (see all 5)
    breast cancer 13.7 18 19707223 (5), 17896178 (3), 16049973 (2), 17311260 (1)
    colorectal cancer 13.3 2 15902326 (1), 17216011 (1)
    cancer lung 0 6 17420066 (4)
    tumors 0 2 9422575 (1), 9757129 (1)
    lymphoma 0 1 12604405 (1)

    Genetic Association Database (GAD): SHMT1
    Human Genome Epidemiology (HuGE) Navigator: SHMT1 (75 documents)

    Export disorders for SHMT1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SHMT1 gene, integrated from 9 sources (see all 168):
    (articles sorted by number of sources associating them with SHMT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Is mutated serine hydroxymethyltransferase (SHMT) involved in the etiology of neural tube defects? (PubMed id 11386852)1, 4, 7, 9 Heil S.G....Blom H.J. (2001)
    2. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PubMed id 8505317)1, 2, 3, 9 Garrow T.A.... Shane B. (1993)
    3. No association between cSHMT genotypes and the risk o f breast cancer in the Nurses' Health Study. (PubMed id 19707223)1, 4, 9 Bentley A.R....Cassano P.A. (2010)
    4. Polymorphisms of cytosolic serine hydroxymethyltransferase and risk of lung cancer: a case-control analysis. (PubMed id 17420066)1, 4, 9 Wang L....Wei Q. (2007)
    5. The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. (PubMed id 9753690)1, 2, 9 Renwick S.B.... Baumann U. (1998)
    6. Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan. (PubMed id 17896178)1, 4, 9 Cheng C.W....Shen C.Y. (2008)
    7. Polymorphisms in cytoplasmic serine hydroxymethyltransferase and methylenetetrahydrofolate reductase affect the risk of cardiovascular disease in men. (PubMed id 16046727)1, 4, 9 Lim U....Cassano P.A. (2005)
    8. Mimosine attenuates serine hydroxymethyltransferase transcription by chelating zinc. Implications for inhibition of DNA replication. (PubMed id 15531579)1, 7, 9 Perry C....Stover P.J. (2005)
    9. Polymorphisms in the one-carbon metabolic pathway, plasma folate levels and colorectal cancer in a prospective study. (PubMed id 15122597)1, 4, 9 Chen J....Ma J. (2004)
    10. Dietary intake of B-vitamins, polymorphisms in thymidylate synthase and serine hydroxymethyltransferase 1, and colorectal adenoma risk: a Dutch case-control study. (PubMed id 17113224)1, 4, 9 van den Donk M....Kampman E. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6470 HGNC: 10850 AceView: SHMT1 Ensembl:ENSG00000176974 euGenes: HUgn6470
    ECgene: SHMT1 Kegg: 6470 H-InvDB: SHMT1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SHMT1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SHMT1 gene:
    Search GeneIP for patents involving SHMT1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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