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

SHMT2 Gene

protein-coding   GIFtS: 65
GCID: GC12P057623

Serine Hydroxymethyltransferase 2 (Mitochondrial)


(Previous symbol: SHMT)
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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Serine Hydroxymethyltransferase 2 (Mitochondrial)1 2     GLY A+2
SHMT1 2 3     Glycine Auxotroph A, Human Complement For Hamster2
Glycine Hydroxymethyltransferase2 3     Serine Aldolase2
Serine Methylase2 3     Serine Hydroxymethylase2
EC 2.1.2.13 8     Serine Hydroxymethyltransferase, Mitochondrial2
GLYA2 5     Threonine Aldolase2

External Ids:    HGNC: 108521   Entrez Gene: 64722   Ensembl: ENSG000001821997   OMIM: 1384505   UniProtKB: P348973   
ORGUL members:         
NONCODE14:n408345 n408346 n408344      

Export aliases for SHMT2 gene to outside databases

Previous GC identifers: GC12U990093 GC12P057340 GC12P055909 GC12P055886 GC12P054662


(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 SHMT2 Gene:
This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible
reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is
primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the
primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on
chromosome 17. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Oct 2009)

GeneCards Summary for SHMT2 Gene: 
SHMT2 (serine hydroxymethyltransferase 2 (mitochondrial)) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with SHMT2 include pyridoxine deficiency, and neural tube defects, and among its related super-pathways are One carbon pool by folate and glycine biosynthesis I. GO annotations related to this gene include methyltransferase activity and identical protein binding. An important paralog of this gene is SHMT1.

UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897
Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil
accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA




(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_000012.11  NC_018923.2  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SHMT2 gene promoter:
         E2F-3a   E2F-1   Sp1   E2F-2   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSHMT2 promoter sequence
   Search SABiosciences Chromatin IP Primers for SHMT2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SHMT2


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

Entrez Gene cytogenetic band: 12q12-q14   Ensembl cytogenetic band:  12q13.3   HGNC cytogenetic band: 12q12-q14

SHMT2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHMT2 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P057623:  view genomic region     (about GC identifiers)

Start:
57,623,110 bp from pter      End:
57,628,718 bp from pter
Size:
5,609 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SHMT2

(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: GLYM_HUMAN, P34897 (See protein sequence)
Recommended Name: Serine hydroxymethyltransferase, mitochondrial precursor  
Size: 504 amino acids; 55993 Da
Cofactor: Pyridoxal phosphate
Subunit: Homotetramer
Subcellular location: Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion inner membrane
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 SHMT2:
3OU5 (3D)    
Secondary accessions: B7Z9F1 E7EQ19 E7EU43 O00740 Q8N1A5
Alternative splicing: 3 isoforms:  P34897-1   P34897-2   P34897-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SHMT2: NX_P34897

Explore proteomics data for SHMT2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P34897

  • 4/22 DME Specific Peptides for SHMT2 (P34897) (see all 22)
     VTTTTHK  LIASENF  LVSGGTD  GGTDNHL 

    SHMT2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SHMT2 Protein Expression
    REFSEQ proteins (5 alternative transcripts): 
    NP_001159828.1  NP_001159829.1  NP_001159830.1  NP_001159831.1  NP_005403.2  

    ENSEMBL proteins: 
     ENSP00000333667   ENSP00000451169   ENSP00000452315   ENSP00000450930   ENSP00000452035  
     ENSP00000450594   ENSP00000451630   ENSP00000450610   ENSP00000406881   ENSP00000450927  
     ENSP00000450452   ENSP00000452161   ENSP00000450893   ENSP00000452045   ENSP00000452419  
     ENSP00000451968   ENSP00000452404   ENSP00000413770   ENSP00000451872   ENSP00000452339  
     ENSP00000451371   ENSP00000452163   ENSP00000451495   ENSP00000450490   ENSP00000377413  

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    Cloud-Clone Corp. Proteins for SHMT2 

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA--
    GO:0005743mitochondrial inner membrane IDA--
    GO:0005758mitochondrial intermembrane space IEA--
    GO:0005759mitochondrial matrix IDA11516159
    GO:0015630microtubule cytoskeleton IDA--

    SHMT2 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 P34897

    ProtoNet protein and cluster: P34897

    1 Blocks protein domain: IPB001085 Glycine hydroxymethyltransferase

    UniProtKB/Swiss-Prot: GLYM_HUMAN, P34897
    Similarity: Belongs to the SHMT family


    SHMT2 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: GLYM_HUMAN, P34897
    Function: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil
    accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA
    Catalytic activity: 5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine

         Genatlas biochemistry entry for SHMT2:
    serine hydroxy-methyltransferase,pyridoxal dependent,mitochondrial,catalyzing 5-10 methylene THF
    synthesis,"one-carbone" metabolism,putative regulator of cell growth and proliferation

         Enzyme Number (IUBMB): EC 2.1.2.11 2

         Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA18063578
    GO:0004372glycine hydroxymethyltransferase activity IDA17482557
    GO:0008168methyltransferase activity ----
    GO:0008732L-allo-threonine aldolase activity IEA--
    GO:0016597amino acid binding IEA--
         
    SHMT2 for ontologies           About GeneDecksing


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    SwitchGear 3'UTR luciferase reporter plasmidSHMT2 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 SHMT2 About   (see all 9)                                                                                              See pathways by source

    SuperPathContained pathways About
    1One Carbon Metabolism
    One carbon pool by folate0.53
    One Carbon Metabolism0.53
    2glycine biosynthesis I
    glycine biosynthesis I0.67
    folate transformations I0.43
    superpathway of serine and glycine biosynthesis I0.67
    dTMP de novo biosynthesis (mitochondrial)0.33
    folate polyglutamylation0.50
    3Carbon metabolism
    Carbon metabolism0.37
    Biosynthesis of amino acids0.37
    4Metabolism
    Metabolic pathways0.40
    5Taurine and hypotaurine metabolism
    Cyanoamino acid metabolism0.31

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for SHMT2
        Glucose / Energy Metabolism

    5/7 BioSystems Pathways for SHMT2 (see all 7)
        One Carbon Metabolism
    dTMP de novo biosynthesis (mitochondrial)
    folate transformations I
    folate polyglutamylation
    glycine betaine degradation



    5/7         Kegg Pathways  (Kegg details for SHMT2) (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: GLYM_HUMAN, P34897
    Pathway: One-carbon metabolism; tetrahydrofolate interconversion


    SHMT2 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SHMT2

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

    5/401 Interacting proteins for SHMT2 (P348972, 3 ENSP000003336674) via UniProtKB, MINT, STRING, and/or I2D (see all 401)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRMT10CQ7L0Y32, 3, ENSP000003123564MINT-8079030 I2D: score=1 STRING: ENSP00000312356
    EEF1A1P681042, 3MINT-8076236 I2D: score=1 
    KARSQ150462, 3MINT-8079030 I2D: score=1 
    CSNK2BP678703, ENSP000003650254I2D: score=2 STRING: ENSP00000365025
    ENSG00000206406P678703I2D: score=2 
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006544glycine metabolic process ----
    GO:0006545glycine biosynthetic process ----
    GO:0006563L-serine metabolic process ----
    GO:0006564L-serine biosynthetic process IEA--
    GO:0006730one-carbon metabolic process IDA11516159

    SHMT2 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

    SHMT2 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for SHMT2 (GLYM)

    6 HMDB Compounds for SHMT2    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--

    3 DrugBank Compounds for SHMT2    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17664250 16876889 17142057 16980404 17355947
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor15865438 11877399 17482557 17651438 16980404
    Tetrahydrofolic acid5,6,7,8-tetrahydrofolate (see all 3)135-16-0targetcofactor9449840 17142057 11386852 17651438 11737206

    10/12 Novoseek inferred chemical compound relationships for SHMT2 gene (see all 12)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    4-deoxypyridoxine 88.7 1 7526359 (1)
    tetrahydrofolate 86.8 3 8786078 (1), 19815026 (1), 15170323 (1)
    pyridoxal 5-phosphate 79.8 14 12913008 (3), 10387080 (3), 19158217 (1), 8405393 (1) (see all 5)
    5,10-methenyltetrahydrofolate 78.4 1 15170323 (1)
    serine 73.2 44 18029478 (2), 8435385 (2), 2127307 (2), 11189372 (2) (see all 26)
    vitamin b6 57.8 5 19158217 (2), 7526359 (1)
    leucovorin 45.7 4 15170323 (2), 15888445 (1)
    folate 44.6 5 15170323 (2), 16137637 (1), 10656824 (1)
    aspartate 33.8 3 10493937 (1), 10656824 (1), 8405393 (1)
    lysine 15.9 1 10387080 (1)

    Search CenterWatch for drugs/clinical trials and news about SHMT2 / GLYM

    (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,
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    About This Section

    REFSEQ mRNAs for SHMT2 gene (5 alternative transcripts): 
    NM_001166356.1  NM_001166357.1  NM_001166358.1  NM_001166359.1  NM_005412.5  

    Unigene Cluster for SHMT2:

    Serine hydroxymethyltransferase 2 (mitochondrial)
    Hs.741179  [show with all ESTs]
    Unigene Representative Sequence: BC004189
    18/36 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 36):
    ENST00000328923(uc001snf.2 uc009zpk.2 uc001sng.2 uc001sni.2 uc010srh.2)
    ENST00000556825(uc001snh.2 uc010srg.2 uc010srj.2) ENST00000557740
    ENST00000554600 ENST00000553324 ENST00000554467 ENST00000557487 ENST00000553950
    ENST00000555634 ENST00000556689 ENST00000557269 ENST00000555563 ENST00000557433
    ENST00000414700 ENST00000557348 ENST00000557703 ENST00000553529 ENST00000554310

    Congresses - knowledge worth sharing:  
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    Additional mRNA sequence: 

    AK223555.1 AK295941.1 AK296183.1 AK297173.1 AK298231.1 AK301339.1 AK301443.1 AK303827.1 
    AK315916.1 BC004189.1 BC008066.2 BC008711.1 BC011911.2 BC013677.2 BC025355.1 BC032584.1 
    BC044211.1 BC091501.1 BT006866.1 BX647711.1 BX648847.1 L11932.1 NR_029415.1 NR_029416.1 
    NR_029417.1 NR_048562.1 

    24/62 DOTS entries (see all 62):

    DT.100803976  DT.91784496  DT.448610  DT.92057266  DT.92065933  DT.121193731  DT.100740502  DT.100886255 
    DT.121193641  DT.101985586  DT.100886226  DT.100886245  DT.91712012  DT.91784339  DT.100886251  DT.92407768 
    DT.121193660  DT.91784666  DT.91855748  DT.100835452  DT.91784458  DT.91784410  DT.91784517  DT.99981974 

    24/1296 AceView cDNA sequences (see all 1296):

    BU728928 BQ057288 BP872320 AA243310 AK094231 CA428887 BI333326 BM787444 
    AW410517 BM834053 BG751864 BM008051 BQ898542 BU680914 CD244165 W73762 
    BM781533 AL552238 BM677703 BG056020 BE266577 CB126698 BM564630 BM744099 

    GeneLoc Exon Structure

    5/38 Alternative Splicing Database (ASD) splice patterns (SP) for SHMT2 (see all 38)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ·
    SP1:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -               
    SP2:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -               
    SP3:                                                                                      -     -     -     -     -     -     -     -     -     -               
    SP4:                                                                                      -     -     -     -     -     -     -     -     -     -               
    SP5:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -           -   

    ExUns: 5d · 5e ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ^ 10a · 10b · 10c · 10d ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^
    SP1:                          -                                                                 -                             -                                 
    SP2:                          -                                                                 -                             -     -                           
    SP3:  -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -                             -                                 
    SP4:                          -                                                                 -                             -                                 
    SP5:  -     -     -     -     -                                                                 -                             -                                 

    ExUns: 14a · 14b · 14c · 14d · 14e ^ 15 ^ 16a · 16b · 16c ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c
    SP1:                                -                                                                                 
    SP2:                                -                                                                                 
    SP3:                                -                                                                                 
    SP4:                                                                                                                  
    SP5:                                                                                                                  


    ECgene alternative splicing isoforms for SHMT2

    (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

    SHMT2 expression in normal human tissues (normalized intensities)      SHMT2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATCACAGTGT
    SHMT2 Expression
    About this image


    SHMT2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/34 selected tissues (see all 34) fully expand
     
     Epithelium (Reproductive System)    fully expand to see all 4 entries
             cervix, uterine ; squamous epithelial cells   
     
     Uterus
             uterus, post-menopause ; glandular cells   
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
             lung ; macrophages   
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Mandibular Condyle
             skeleton/cranium/viscerocranium   

    See SHMT2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SHMT2

    SOURCE GeneReport for Unigene cluster: Hs.741179
        SABiosciences Expression via Pathway-Focused PCR Array including SHMT2: 
              Amino Acid Metabolism II in human mouse rat

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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 SHMT2 gene from 9/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Shmt21 , 5 serine hydroxymethyltransferase 2 (mitochondrial)1, 5 87.87(n)1
    94.04(a)1
      10 (74.51 cM)5
    1080371  NM_028230.41  NP_082506.11 
     1275171235 
    lizard
    (Anolis carolinensis)
    Reptilia SHMT26
    serine hydroxymethyltransferase 2 (mitochondrial)
    82(a)
    1 ↔ 1
    GL343212.1(1740134-1769844)
    African clawed frog
    (Xenopus laevis)
    Amphibia BX853756.12   -- 76.63(n)    BX853756.1 
    zebrafish
    (Danio rerio)
    Actinopterygii shmt21 serine hydroxymethyltransferase 2 (mitochondrial) 71.75(n)
    78.05(a)
      100144628  NM_001123374.1  NP_001116846.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG30113 glycine hydroxymethyltransferase 60(a)   5C7   --
    worm
    (Caenorhabditis elegans)
    Secernentea mel-323   -- 57(a)   III(6512024-6514577)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SHM1(YBR263W)4
    SHM21
    Mitochondrial serine hydroxymethyltransferase, converts more4
    Shm2p1
    56.75(n)1
    56.6(a)1
      2(736264-737736)4
    8507471  NP_013159.11  8525654 
     NP_009822.24 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SHM21 serine hydroxymethyltransferase 2 57.52(n)
    59.92(a)
      832736  NM_180750.2  NP_851081.1 
    rice
    (Oryza sativa)
    Liliopsida Os.121482 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 74.3(n)    AK100404.1 


    ENSEMBL Gene Tree for SHMT2 (if available)
    TreeFam Gene Tree for SHMT2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SHMT2 gene
    SHMT12  
    3 SIMAP similar genes for SHMT2 using alignment to 17 protein entries:     GLYM_HUMAN (see all proteins):
    DKFZp686P09201    SHMT1    SHMT

    SHMT2 for paralogs           About GeneDecksing



    (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

    10/212 SNPs in SHMT2 are shown (see all 212)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1149576411,2
    F--57455437(+) GCTACA/GGTAAA 3 -- us2k11Minor allele frequency- G:0.02WA 118
    rs1156493881,2
    F--57455830(+) ACTCCC/TACTGC 5 -- us2k11Minor allele frequency- T:0.02WA 118
    rs1919335691,2
    --57455989(+) TCTACC/TAAAAA 5 -- us2k10--------
    rs1512444511,2
    --57456013(+) CTGGAC/TGTGGT 5 -- us2k10--------
    rs767585081,2
    C,F--57456093(+) GGTTGC/TAGTGA 7 -- us2k12Minor allele frequency- T:0.50WA CSA 4
    rs1132638341,2
    C--57456165(+) AAAAC-/AAAAAA 9 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1445105751,2
    C--57456218(+) AGTGCA/GGTGGC 9 -- us2k10--------
    rs1180435231,2
    F--57456322(+) TAGGTA/GATTTA 9 -- us2k11Minor allele frequency- G:0.01EA 120
    rs128261781,2
    C,F--57456345(+) ttgtaG/Tagata 9 -- us2k1 tfbs34Minor allele frequency- T:0.10NA 126
    rs1831367041,2
    --57456377(+) GCTGGC/TTTAGA 9 -- us2k10--------

    HapMap Linkage Disequilibrium report for SHMT2 (57623110 - 57628718 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SHMT2:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv899116CNV Loss21882294
    dgv96n21CNV Loss19592680
    nsv519293CNV Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 138450    OMIM disorders: --

    6 diseases for SHMT2:    About MalaCards
    pyridoxine deficiency    neural tube defects    pneumonia    tuberculosis
    prostate cancer    prostatitis


    SHMT2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SHMT2
    Human Genome Epidemiology (HuGE) Navigator: SHMT2 (9 documents)

    Export disorders for SHMT2 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 SHMT2 gene, integrated from 9 sources (see all 96):
    (articles sorted by number of sources associating them with SHMT2)
        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 Heil S.G....Blom H.J. (2001)
    2. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. (PubMed id 8999870)1, 2, 3 Stover P.J.... Shane B. (1997)
    3. Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization. (PubMed id 8505317)1, 2, 9 Garrow T.A.... Shane B. (1993)
    4. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (2010)
    5. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    6. Oral facial clefts and gene polymorphisms in metabolism of folate/one-carbon and vitamin A: a pathway-wide association study. (PubMed id 19048631)1, 4 Boyles A.L....Lie R.T. (2009)
    7. MALDI-TOF MS genotyping of polymorphisms related to 1-carbon metabolism using common and mass-modified terminators. (PubMed id 18988749)1, 4 Meyer K....Ueland P.M. (2009)
    8. Polymorphisms in the estrogen receptor 1 and vitamin C and matrix metalloproteinase gene families are associated with susceptibility to lymphoma. (PubMed id 18636124)1, 4 Skibola C.F....Smith M.T. (2008)
    9. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PubMed id 19086053)1, 4 GratacA^s M....Carracedo A. (2008)
    10. The layered structure of human mitochondrial DNA nucleoids. (PubMed id 18063578)1, 2 Bogenhagen D.F....Burke S. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    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: 6472 HGNC: 10852 AceView: SHMT2andNXPH4 Ensembl:ENSG00000182199 euGenes: HUgn6472
    ECgene: SHMT2 Kegg: 6472 H-InvDB: SHMT2

    (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 SHMT2 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 SHMT2 gene:
    Search GeneIP for patents involving SHMT2

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



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