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PHGDH Gene

protein-coding   GIFtS: 69
GCID: GC01P120202

Phosphoglycerate Dehydrogenase

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Phosphoglycerate Dehydrogenase1 2     PGD2
3-PGDH2 3     PGDH2
EC 1.1.1.953 8     SERA2
3-Phosphoglycerate Dehydrogenase2     D-3-Phosphoglycerate Dehydrogenase2
3PGDH2     Epididymis Secretory Protein Li 1132
HEL-S-1132     PGDH33
PDG2     EC 1.1.18
PGAD2     

External Ids:    HGNC: 89231   Entrez Gene: 262272   Ensembl: ENSG000000926217   OMIM: 6068795   UniProtKB: O431753   

Export aliases for PHGDH gene to outside databases

Previous GC identifers: GC01P120701 GC01P119092 GC01P119401 GC01P119600 GC01P119966 GC01P120056 GC01P118112


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PHGDH Gene:
This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine
is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms
homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly,
psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found,
however the full-length nature of most are not known. (provided by RefSeq, Aug 2011)

GeneCards Summary for PHGDH Gene:
PHGDH (phosphoglycerate dehydrogenase) is a protein-coding gene. Diseases associated with PHGDH include phgdh deficiency, and serine deficiency. GO annotations related to this gene include phosphoglycerate dehydrogenase activity and electron carrier activity. An important paralog of this gene is CTBP1.

Gene Wiki entry for PHGDH (Phosphoglycerate dehydrogenase) Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the PHGDH gene promoter:
         GR   Max1   IRF-1   CUTL1   PPAR-alpha   Max   NRF-2   GR-alpha   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 4): PHGDH promoter sequence
   Search Chromatin IP Primers for PHGDH

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PHGDH


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

Entrez Gene cytogenetic band: 1p12   Ensembl cytogenetic band:  1p12   HGNC cytogenetic band: 1p12

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P120202:  view genomic region     (about GC identifiers)

Start:
120,202,421 bp from pter      End:
120,286,849 bp from pter
Size:
84,429 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SERA_HUMAN, O43175 (See protein sequence)
Recommended Name: D-3-phosphoglycerate dehydrogenase  
Size: 533 amino acids; 56651 Da
Subunit: Homotetramer (By similarity)
1 PDB 3D structure from and Proteopedia for PHGDH:
2G76 (3D)    
Secondary accessions: B2RD08 Q5SZU3 Q9BQ01

Explore the universe of human proteins at neXtProt for PHGDH: NX_O43175

Explore proteomics data for PHGDH at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys21, Lys33, Lys38, Lys58, Lys146, Lys289, Lys351, Lys364, Lys380, Lys384,
                                 Lys394
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for PHGDH (O43175) (see all 19)
     PHLGAST  GREVATR  LLSYQTS  AWAGSPKG 


    See PHGDH Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006614.2  
    ENSEMBL proteins: 
     ENSP00000358417   ENSP00000358415  
    Reactome Protein details: O43175

    PHGDH Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for PHGDH
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    Novus Biologicals PHGDH Protein
    Novus Biologicals PHGDH Lysates
    Sino Biological Recombinant Protein for PHGDH
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PHGDH

    PHGDH Antibody Products:

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    LSBio Antibodies in human, mouse, rat for PHGDH

    PHGDH Assay Products:

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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for PHGDH
    Cloud-Clone Corp. CLIAs for PHGDH


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR006236 D-3-Phosphoglycerate_DH
     IPR006140 D-isomer_2_OHA_DH_NAD-bd
     IPR006139 D-isomer_2_OHA_DH_cat_dom
     IPR016040 NAD(P)-bd_dom

    Graphical View of Domain Structure for InterPro Entry O43175

    ProtoNet protein and cluster: O43175

    2 Blocks protein domains:
    IPB001588 Casein
    IPB006139 D-isomer specific 2-hydroxyacid dehydrogenase


    UniProtKB/Swiss-Prot: SERA_HUMAN, O43175
    Similarity: Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family


    PHGDH 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SERA_HUMAN, O43175
    Catalytic activity: 3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
    Catalytic activity: 2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
    Biophysicochemical properties: Kinetic parameters: KM=21.6 uM for 3-phosphohydroxypyruvate; Vmax=35 nmol/min/mg
    enzyme with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts); Vmax=168 nmol/min/mg enzyme
    with 3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells);
    Induction: Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand).
    Positively regulated by the transcription factors SP1 and NF-Y

         Enzyme Numbers (IUBMB): EC 1.1.1.951 2 EC 1.1.12

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004617phosphoglycerate dehydrogenase activity TAS--
    GO:0009055electron carrier activity TAS8758134
    GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ----
    GO:0048037cofactor binding ----
    GO:0051287NAD binding IEA--
         
    PHGDH for ontologies           About GeneDecksing


    Phenotypes:
         9 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Phgdh):
     cellular  craniofacial  embryogenesis  growth/size/body  homeostasis/metabolism 
     limbs/digits/tail  mortality/aging  nervous system  tumorigenesis 

    PHGDH for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Phgdhtm1.1Shfu for PHGDH

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PHGDH
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for PHGDH

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PHGDH
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PHGDH

    miRNA
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    miRTarBase miRNAs that target PHGDH:
    hsa-mir-615-3p (MIRT039728), hsa-mir-155-5p (MIRT020945), hsa-mir-107 (MIRT048300), hsa-mir-26b-5p (MIRT030040), hsa-mir-331-3p (MIRT043507), hsa-mir-296-3p (MIRT038390), hsa-mir-1229-3p (MIRT036377)

    Block miRNA regulation of human, mouse, rat PHGDH using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate PHGDH:
    hsa-miR-128 hsa-miR-3681*
    SwitchGear 3'UTR luciferase reporter plasmidPHGDH 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat PHGDH

    Gene Editing
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    GenScript: all cDNA clones in your preferred vector: PHGDH (NM_006623)
    Sino Biological Human cDNA Clone for PHGDH
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PHGDH
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PHGDH

    Cell Line
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PHGDH


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol4
    plasma membrane3
    mitochondrion2
    cytoskeleton1
    endoplasmic reticulum1
    extracellular1
    nucleus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol TAS--
    GO:0070062extracellular vesicular exosome IDA19056867

    PHGDH for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for PHGDH About    
    See pathways by source

    SuperPathContained pathways About
    1Metabolism
    Metabolism0.38
    Metabolic pathways0.38
    2Metabolism of amino acids and derivatives
    Metabolism of amino acids and derivatives
    Amino acid synthesis and interconversion (transamination)0.00
    Serine biosynthesis0.00
    3Carbon metabolism
    Carbon metabolism0.38
    Biosynthesis of amino acids0.38
    4One carbon pool by folate
    Trans-sulfuration and one carbon metabolism0.43
    5Glycine, serine and threonine metabolism
    Glycine, serine and threonine metabolism

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for PHGDH
        Trans-sulfuration and one carbon metabolism


    1 Reactome Pathway for PHGDH
        Serine biosynthesis


    4 Kegg Pathways  (Kegg details for PHGDH):
        Glycine, serine and threonine metabolism
    Metabolic pathways
    Carbon metabolism
    Biosynthesis of amino acids

    UniProtKB/Swiss-Prot: SERA_HUMAN, O43175
    Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3


    PHGDH for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including PHGDH: 

              Multiple Sclerosis in human mouse rat
              Amino Acid Metabolism II in human mouse rat
              GABA & Glutamate in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for PHGDH

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

    Selected Interacting proteins for PHGDH (O431752, 3 ENSP000003584174) via UniProtKB, MINT, STRING, and/or I2D (see all 906)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ETF1P624952, 3, ENSP000003537414MINT-7945693 MINT-7947479 I2D: score=6 STRING: ENSP00000353741
    CHEK1O147572, 3MINT-7945693 MINT-7947479 I2D: score=5 
    PSMC4P436862, 3MINT-7945693 MINT-7947479 I2D: score=5 
    RBBP5Q152912, 3MINT-7945693 MINT-7947479 I2D: score=5 
    ENSG00000258947Q135092, 3MINT-7945693 I2D: score=4 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006541glutamine metabolic process IEA--
    GO:0006544glycine metabolic process IEA--
    GO:0006563L-serine metabolic process ----
    GO:0006564L-serine biosynthetic process TAS--
    GO:0006566threonine metabolic process IEA--

    PHGDH for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PHGDH (SERA)

    5 HMDB Compounds for PHGDH    About this table
    CompoundSynonyms CAS #PubMed Ids
    3-Phosphoglyceric acid3-(dihydrogen phosphate)Glycerate (see all 21)820-11-1--
    NAD3-Carbamoyl-1-D-ribofuranosylpyridinium hydroxide 5'-ester with adenosine 5'-pyrophosphate (see all 28)53-84-9--
    NADH1,4-Dihydronicotinamide adenine dinucleotide (see all 17)58-68-4--
    Oxoglutaric acid2-Ketoglutarate (see all 9)328-50-7--
    Phosphohydroxypyruvic acid2-oxo-3-(phosphonooxy)-Propanoate (see all 8)3913-50-6--

    1 DrugBank Compound for PHGDH    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    NADHbeta-DPNH (see all 18)606-68-8target--945314 17139284 17016423 2692566 12183470

    8 Novoseek inferred chemical compound relationships for PHGDH gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    3-phosphoglycerate 96.6 68 9163325 (4), 11034457 (3), 11571699 (3), 9708551 (2) (see all 32)
    3-phosphohydroxypyruvate 94.7 2 18378410 (1)
    serine 74 65 18296366 (5), 9708551 (3), 11055895 (3), 17068790 (2) (see all 27)
    phosphoserine 56.8 3 16763900 (1), 10222452 (1), 8739971 (1)
    5-methyltetrahydrofolate 53.1 1 11508546 (1)
    alpha-ketoglutarate 47.1 2 9163325 (1), 8550422 (1)
    nadh 38.7 1 19388702 (1)
    purine 22 1 10222208 (1)



    PHGDH for compounds           About GeneDecksing



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PHGDH gene: 
    NM_006623.3  

    Unigene Cluster for PHGDH:

    Phosphoglycerate dehydrogenase
    Hs.487296  [show with all ESTs]
    Unigene Representative Sequence: AK093306
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000493622 ENST00000496756 ENST00000369409(uc009whl.3 uc001ehz.3 uc009whm.3)
    ENST00000462324 ENST00000369407(uc001eib.3) ENST00000469443 ENST00000482968

    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate PHGDH:
    hsa-miR-128 hsa-miR-3681*
    SwitchGear 3'UTR luciferase reporter plasmidPHGDH 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat PHGDH
      QuantiFast Probe-based Assays in human, mouse, rat PHGDH

    Additional mRNA sequence: 

    AF171235.1 AF171236.1 AF171237.1 AK093306.1 AK129762.1 AK309662.1 AK310132.1 AK315360.1 
    BC000303.2 BC001349.2 BC011262.1 BC023235.1 BC032110.2 CR456795.1 

    Selected DOTS entries (see all 46):

    DT.87017070  DT.92470699  DT.100689962  DT.100689953  DT.100689970  DT.121442379  DT.92470705  DT.95357891 
    DT.100689941  DT.100689969  DT.91985641  DT.95357924  DT.100689967  DT.121442325  DT.100689954  DT.101987501 
    DT.95357876  DT.100689976  DT.121442264  DT.92470724  DT.97861052  DT.100639300  DT.100639301  DT.121442309 

    Selected AceView cDNA sequences (see all 1066):

    BP349483 BQ918740 AU121923 BM773151 BQ685488 AA226966 BQ688979 BM792784 
    BM833769 BQ056044 AU143765 BG107457 AA844271 BM827736 AU125672 BM756668 
    BU553399 BG764898 AU116963 AI085499 BE794265 BQ883369 AI004352 BP360999 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PHGDH (see all 15)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b ^
    SP1:                    -     -                                         -     -     -                       -     -                                             
    SP2:                                                                    -     -     -                       -     -                                             
    SP3:                    -     -     -                                   -     -     -                       -     -                                             
    SP4:                    -     -     -     -                             -     -     -                       -     -                                             
    SP5:                    -     -                                         -     -     -                       -                                                   

    ExUns: 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c
    SP1:  -                 -                           
    SP2:  -                 -                           
    SP3:                                                
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for PHGDH

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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


    PHGDH expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Brain (Nervous System)    fully expand to see all 7 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Adipose (Muscoskeletal System)
             Visceral White Adipose
     
     Thymus (Hematopoietic System)
             Thymus
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
    PHGDH Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PHGDH Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.487296
        Pathway & Disease-focused RT2 Profiler PCR Arrays including PHGDH: 
              Multiple Sclerosis in human mouse rat
              Amino Acid Metabolism II in human mouse rat
              GABA & Glutamate 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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for PHGDH gene from Selected species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phgdh1 , 5 3-phosphoglycerate dehydrogenase1, 5 88.06(n)1
    94.56(a)1
      3 (42.74 cM)5
    2365391  NM_016966.31  NP_058662.21 
     983131705 
    chicken
    (Gallus gallus)
    Aves PHGDH1 phosphoglycerate dehydrogenase 68.83(n)
    68.19(a)
      424381  XM_422226.4  XP_422226.2 
    lizard
    (Anolis carolinensis)
    Reptilia PHGDH6
    phosphoglycerate dehydrogenase
    68(a)
    1 ↔ 1
    GL343782.1(135001-158400)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.200622 Transcribed sequence with weak similarity to protein more 73.87(n)    CF785148.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb38f062 wufb38f06 76.52(n)   321928  BC056334.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG62871 , 3 phosphoglycerate dehydrogenase3
    CG62871
    52(a)3
    57.1(n)1
    54.26(a)1
      32D53
    345541  NM_135652.21  NP_609496.11 
    worm
    (Caenorhabditis elegans)
    Secernentea C31C9.23
    CELE_C31C9.21
    D-3-Phosphoglycerate dehydrogenase3
    CELE_C31C9.21
    53(a)3
    57.67(n)1
    54.29(a)1
      II(13636986-13638371)3
    1750121  NM_064467.51  NP_496868.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SER33(YIL074C)4 3-phosphoglycerate dehydrogenase, catalyzes the first more   --   9(222490-221081) 854736  NP_012191.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons EDA91 EDA9 51.94(n)
    44.44(a)
      829568  NM_119583.3  NP_195146.1 
    rice
    (Oryza sativa)
    Liliopsida Os04g06508001 Os04g0650800 51.35(n)
    44.7(a)
      4337230  NM_001060629.1  NP_001054094.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PHGDH gene
    CTBP12  CTBP22  ENSG000002128842  
    2 SIMAP similar genes for PHGDH using alignment to 3 protein entries:     SERA_HUMAN (see all proteins):
    PGDH3    GRHPR

    PHGDH 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PHGDH (see all 775)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1219079871,2,,4
    CPhosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4 pathogenic1120358200(+) CAGGCA/GTGCGG 2 M V mis10--------
    VAR_0590284
    Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4--see VAR_0590282 A T mis40--------
    VAR_0590264
    Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4--see VAR_0590262 R W mis40--------
    VAR_0590294
    Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4--see VAR_0590292 G S mis40--------
    VAR_0134614
    Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4--see VAR_0134612 V M mis40--------
    VAR_0590274
    Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency)4--see VAR_0590272 V M mis40--------
    rs1892736601,2
    --118111009(+) GTCTTA/GTGTGT 1 -- us2k10--------
    rs343272211,2
    C--118125820(+) TTTTT-/T/TT  
            
    GAGTA
    1 -- int12NA CSA 4
    rs723079201,2
    C--118127344(+) GAAGA-/GTGT  
            
    GTGTG
    1 -- int10--------
    rs1464103771,2
    C--118127344(+) GAAGA-/GTGTGTG 1 -- int10--------

    HapMap Linkage Disequilibrium report for PHGDH (120202421 - 120286849 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for PHGDH:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831215CNV Gain17160897
    nsv524681CNV Gain19592680
    nsv428201CNV Gain18775914
    nsv831204CNV Gain+Loss17160897
    dgv94e1CNV Complex17122850
    dgv93e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): PHGDH
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PHGDH
    DNA2.0 Custom Variant and Variant Library Synthesis for PHGDH

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606879   
    OMIM disorders: 601815  
    UniProtKB/Swiss-Prot: SERA_HUMAN, O43175
  • Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:601815]: Characterized by congenital
    microcephaly, psychomotor retardation, and seizures. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • Selected diseases for PHGDH (see all 30):    
    About MalaCards
    phgdh deficiency    serine deficiency    mixed malaria    scarlet fever
    cerebral folate deficiency    erysipelas    ornithosis    west syndrome
    2-hydroxyglutaric aciduria    microcephaly    anovulation    typhoid fever
    autoimmune hepatitis    keloids    malaria    tuberculosis
    labyrinthitis    cerebritis    astrocytoma    multiple sclerosis

    3 diseases from the University of Copenhagen DISEASES database for PHGDH:
    Serine deficiency     Microcephaly     Anovulation

    PHGDH for disorders           About GeneDecksing

    3 Novoseek inferred disease relationships for PHGDH gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    microcephaly 83.8 12 20196394 (2), 16763900 (1), 15610810 (1), 11055895 (1) (see all 8)
    tuberculosis 19.9 11 15668250 (4), 19388702 (2), 17761677 (2), 18627175 (2)
    shock 11.1 4 15606508 (1), 2115888 (1), 18310271 (1), 18334753 (1)

    Genetic Association Database (GAD): PHGDH
    Human Genome Epidemiology (HuGE) Navigator: PHGDH (2 documents)

    Export disorders for PHGDH 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)
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    PubMed articles for PHGDH gene, integrated from 10 sources (see all 111):
    (articles sorted by number of sources associating them with PHGDH)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. (PubMed id 19235232)1, 2, 9 Tabatabaie L.... Klomp L.W.J. (Hum. Mutat. 2009)
    2. Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L- serine biosynthesis. (PubMed id 11055895)1, 2, 9 Klomp L.W.J.... Berger R. (Am. J. Hum. Genet. 2000)
    3. V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. (PubMed id 11751922)1, 2, 9 Pind S.... Natowicz M.R. (J. Biol. Chem. 2002)
    4. Nucleotide sequence and differential expression of the human 3- phosphoglycerate dehydrogenase gene. (PubMed id 10713460)1, 2, 9 Cho H.M.... Kim Y.H. (Gene 2000)
    5. Human metabolic individuality in biomedical and pharmaceutical research. (PubMed id 21886157)1, 4 Suhre K....Gieger C. (Nature 2011)
    6. Association analysis of glycine- and serine-related genes in a Japanese population of patients with schizophrenia. (PubMed id 19223009)1, 4 Ohnuma T....Arai H. (amp 2009)
    7. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. 3-Phosphoglycerate dehydrogenase expression is regulated by HOXA10 in murine endometrium and human endometrial cells. (PubMed id 19778996)1, 9 Du H....Taylor H.S. (Reproduction 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 26227 HGNC: 8923 AceView: PHGDH Ensembl:ENSG00000092621 euGenes: HUgn26227
    ECgene: PHGDH Kegg: 26227 H-InvDB: PHGDH

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for PHGDH Pharmacogenomics, SNPs, Pathways

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

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



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