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GLDC Gene

protein-coding   GIFtS: 67
GCID: GC09M006522

Glycine Dehydrogenase (Decarboxylating)

(Previous names: glycine dehydrogenase (decarboxylating; glycine decarboxylase,...)
  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
Glycine Dehydrogenase (Decarboxylating)1 2     HYGN12 5
GCSP2 3 5     Glycine Dehydrogenase (Decarboxylating; Glycine Decarboxylase, Glycine
Cleavage System Protein P)1
Glycine Decarboxylase1 3     Glycine Decarboxylase P-Protein2
Glycine Cleavage System Protein P1 2     Glycine Dehydrogenase (Decarboxylating), Mitochondrial2
Glycine Dehydrogenase (Aminomethyl-Transferring)2 3     Glycine Dehydrogenase [Decarboxylating], Mitochondrial2
EC 1.4.4.23 8     Glycine Cleavage System P Protein3
GCE2 5     NKH5

External Ids:    HGNC: 43131   Entrez Gene: 27312   Ensembl: ENSG000001784457   OMIM: 2383005   UniProtKB: P233783   

Export aliases for GLDC gene to outside databases

Previous GC identifers: GC09M006686 GC09M006513


(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 GLDC Gene:
Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial
protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic
acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide
dehydrogenase). The protein encoded by this gene is the P protein, which binds to glycine and enables the
methylamine group from glycine to be transferred to the T protein. Defects in this gene are a cause of nonketotic
hyperglycinemia (NKH).(provided by RefSeq, Jan 2010)

GeneCards Summary for GLDC Gene:
GLDC (glycine dehydrogenase (decarboxylating)) is a protein-coding gene. Diseases associated with GLDC include gldc-related glycine encephalopathy, and infantile glycine encephalopathy. GO annotations related to this gene include electron carrier activity and lyase activity.

UniProtKB/Swiss-Prot: GCSP_HUMAN, P23378
Function: The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino
group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety
is then transferred to the lipoamide cofactor of the H protein

Gene Wiki entry for GLDC (Glycine 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_000009.12  NC_018920.2  NT_008413.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the GLDC gene promoter:
         LHX3b/Lhx3b   Pax-5   Pax-2   MyoD   CUTL1   Pax-2a   C/EBPalpha   AREB6   Pax-2b   LHX3a/Lhx3a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidGLDC promoter sequence
   Search Chromatin IP Primers for GLDC

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


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

Entrez Gene cytogenetic band: 9p22   Ensembl cytogenetic band:  9p24.1   HGNC cytogenetic band: 9p22

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

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M006522:  view genomic region     (about GC identifiers)

Start:
6,532,464 bp from pter      End:
6,645,692 bp from pter
Size:
113,229 bases      Orientation:
minus 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: GCSP_HUMAN, P23378 (See protein sequence)
Recommended Name: Glycine dehydrogenase (decarboxylating), mitochondrial precursor  
Size: 1020 amino acids; 112730 Da
Cofactor: Pyridoxal phosphate
Subunit: Homodimer. The glycine cleavage system is composed of four proteins: P, T, L and H
Secondary accessions: Q2M2F8

Explore the universe of human proteins at neXtProt for GLDC: NX_P23378

Explore proteomics data for GLDC at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys447
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for GLDC (P23378) (see all 36)
     GSSQRFG  WDRPYSR  DGANMNA  GPIGVKK 


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

    REFSEQ proteins: NP_000161.2  
    ENSEMBL proteins: 
     ENSP00000370737  

    GLDC Human Recombinant Protein Products:

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    GLDC Assay Products:

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    Cloud-Clone Corp. ELISAs for GLDC
    Cloud-Clone Corp. CLIAs for GLDC


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 6):
     IPR020581 GDC_P
     IPR001597 ArAA_b-elim_lyase/Thr_aldolase
     IPR020580 GDC-P_N
     IPR003437 GDC_P_homo
     IPR015424 PyrdxlP-dep_Trfase

    Graphical View of Domain Structure for InterPro Entry P23378

    ProtoNet protein and cluster: P23378

    1 Blocks protein domain: IPB003437 Glycine cleavage system P-protein

    UniProtKB/Swiss-Prot: GCSP_HUMAN, P23378
    Similarity: Belongs to the GcvP family


    GLDC 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: GCSP_HUMAN, P23378
    Function: The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino
    group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety
    is then transferred to the lipoamide cofactor of the H protein
    Catalytic activity: Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage
    complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO(2)

         Genatlas biochemistry entry for GLDC:
    glycine decarboxylase pyridoxal-phosphate dependent 120kDa,P protein,catalyzing the first step of the glycine
    cleavage system

         Enzyme Number (IUBMB): EC 1.4.4.21 2

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004375glycine dehydrogenase (decarboxylating) activity IEA--
    GO:0009055electron carrier activity TAS2268343
    GO:0016829lyase activity IEA--
    GO:0030170pyridoxal phosphate binding IEA--
         
    GLDC for ontologies           About GeneDecksing


    Phenotypes:
         6 MGI mutant phenotypes (inferred from 1 allele(MGI details for Gldc):
     craniofacial  embryogenesis  growth/size/body  homeostasis/metabolism  mortality/aging 
     nervous system 

    GLDC for phenotypes           About GeneDecksing

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

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

    miRNA
    Products:
        
    miRTarBase miRNAs that target GLDC:
    hsa-mir-423-3p (MIRT042509)

    Block miRNA regulation of human, mouse, rat GLDC using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate GLDC (see all 11):
    hsa-miR-30c hsa-miR-3163 hsa-miR-146b-3p hsa-miR-30d hsa-miR-410 hsa-miR-188-3p hsa-miR-144 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidGLDC 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for GLDC
    Predesigned siRNA for gene silencing in human, mouse, rat GLDC

    Gene Editing
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat GLDC

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for GLDC 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for GLDC


    (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 UniProtKB/Swiss-Prot
    GCSP_HUMAN, P23378: Mitochondrion
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    chloroplast2
    cytosol1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--

    GLDC 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 GLDC About    
    See pathways by source

    SuperPathContained pathways About
    1glycine cleavage
    glycine cleavage
    glycine biosynthesis II0.00
    2Carbon metabolism
    Carbon metabolism0.38
    3Metabolism
    Metabolic pathways0.38
    4Glycine, serine and threonine metabolism
    Glycine, serine and threonine metabolism
    5Glucose / Energy Metabolism
    Glucose / Energy Metabolism

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


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

    2 BioSystems Pathways for GLDC
        glycine cleavage
    glycine biosynthesis II


    3 Kegg Pathways  (Kegg details for GLDC):
        Glycine, serine and threonine metabolism
    Metabolic pathways
    Carbon metabolism


    GLDC for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including GLDC: 
              Amino Acid Metabolism II in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for GLDC

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

    Selected Interacting proteins for GLDC (P233782, 3 ENSP000003707374) via UniProtKB, MINT, STRING, and/or I2D (see all 291)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GRPEL1Q9HAV72, 3MINT-8079030 I2D: score=1 
    DLDP096222, 3, ENSP000002054024MINT-8079030 I2D: score=1 STRING: ENSP00000205402
    HSPD1P108092, 3, ENSP000003400194MINT-8079030 I2D: score=3 STRING: ENSP00000340019
    TLR10Q9BXR53, ENSP000003089254I2D: score=2 STRING: ENSP00000308925
    TNIP3Q96KP63, ENSP000000575134I2D: score=1 STRING: ENSP00000057513
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006520cellular amino acid metabolic process ----
    GO:0006544glycine metabolic process ----
    GO:0006546glycine catabolic process IEA--
    GO:0055114oxidation-reduction process ----

    GLDC 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 GLDC (GCSP)

    7 HMDB Compounds for GLDC    About this table
    CompoundSynonyms CAS #PubMed Ids
    Carbon dioxideCarbon oxide (see all 5)124-38-9--
    Glycine2-Aminoacetate (see all 15)56-40-6--
    LipoamideLipozyme (see all 25)940-69-2--
    MethylamineAminomethane (see all 21)74-89-5--
    Pyridoxal3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde (see all 3)66-72-8--
    Pyridoxal 5'-phosphateApolon B6 (see all 27)54-47-7--
    S-aminomethyldihydrolipoamide8-[(aminomethyl)sulfanyl]-6-sulfanyloctanamide ----

    2 DrugBank Compounds for GLDC    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Glycine2-Aminoacetic acid (see all 4)56-40-6target--17496108 17361008 17158739
    Pyridoxal PhosphateCodecarboxylase (see all 9)54-47-7targetcofactor16228305 15791207

    9 Novoseek inferred chemical compound relationships for GLDC gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    saci 66.7 2 1943691 (1), 1671321 (1)
    dihydrolipoamide 63.5 1 15946682 (1)
    alpha lipoic acid 61.3 1 11286922 (1)
    tetrahydrofolate 60 1 11286922 (1)
    polyglycolic acid 54.6 2 16358787 (1), 10375564 (1)
    methionine 40.7 1 15864413 (1)
    nitrate 24.7 2 11514514 (1), 15207493 (1)
    carbon 3.37 2 8647275 (2)
    fatty acid 0 1 15207493 (1)



    GLDC 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 GLDC gene: 
    NM_000170.2  

    Unigene Cluster for GLDC:

    Glycine dehydrogenase (decarboxylating)
    Hs.584238  [show with all ESTs]
    Unigene Representative Sequence: NM_000170
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000321612(uc003zkc.3) ENST00000477960 ENST00000467946 ENST00000460457
    ENST00000463305
    miRNA
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    Block miRNA regulation of human, mouse, rat GLDC using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate GLDC (see all 11):
    hsa-miR-30c hsa-miR-3163 hsa-miR-146b-3p hsa-miR-30d hsa-miR-410 hsa-miR-188-3p hsa-miR-144 hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidGLDC 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat GLDC
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    GenScript: all cDNA clones in your preferred vector: GLDC (NM_000170)
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat GLDC
      QuantiTect SYBR Green Assays in human, mouse, rat GLDC
      QuantiFast Probe-based Assays in human, mouse, rat GLDC

    Additional mRNA sequence: 

    AK308470.1 AK310534.1 AK314156.1 BC111993.1 BC111995.1 D90239.1 M63635.1 M64590.1 

    9 DOTS entries:

    DT.213965  DT.95357371  DT.121229099  DT.121194184  DT.75176923  DT.97808198  DT.95163593  DT.101973864 
    DT.40105780 

    Selected AceView cDNA sequences (see all 107):

    BG675043 AI625793 F05755 AU130455 BF685886 CB161786 AV659118 R94124 
    AU124921 AW593954 AW241569 BI006823 AI632186 BX094481 BM556699 AV654845 
    AW204796 AA305450 AA350657 AI431894 BF061978 F07885 BG696971 BE280944 

    GeneLoc Exon Structure


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


    GLDC expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 7 entries
             hIPS1
     
     Liver (Hepatobiliary System)    fully expand to see all 2 entries
             Periportal Hepatocytes Liver Lobule
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             Metanephros
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Midbrain tegmentum
    GLDC Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    GLDC Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.584238
        Pathway & Disease-focused RT2 Profiler PCR Array including GLDC: 
              Amino Acid Metabolism II in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for GLDC
    OriGene qSTAR qPCR primer pairs in human, mouse for GLDC
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat GLDC
    QuantiTect SYBR Green Assays in human, mouse, rat GLDC
    QuantiFast Probe-based Assays in human, mouse, rat GLDC
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for GLDC

    (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

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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for GLDC gene from Selected species (see all 28)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Gldc1 , 5 glycine decarboxylase1, 5 86.94(n)1
    93.2(a)1
      19 (24.87 cM)5
    1041741  NM_138595.21  NP_613061.11 
     300984495 
    chicken
    (Gallus gallus)
    Aves GLDC1 glycine dehydrogenase (decarboxylating) 77.7(n)
    85.06(a)
      374222  NM_204322.1  NP_989653.1 
    lizard
    (Anolis carolinensis)
    Reptilia GLDC6
    glycine dehydrogenase (decarboxylating)
    83(a)
    1 ↔ 1
    2(52713459-52765499)
    African clawed frog
    (Xenopus laevis)
    Amphibia gldc-prov2 glycine dehydrogenase (decarboxylating; glycine decarboxylase, more 77.37(n)    BC042245.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufb23b052 wufb23b05 77.25(n)   321621  BC057478.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG39991 , 3 glycine dehydrogenase
    (decarboxylating)3
    CG39991
    64(a)3
    61.86(n)1
    64.56(a)1
      86A23
    412531  NM_141732.21  NP_649989.11 
    worm
    (Caenorhabditis elegans)
    Secernentea R12C12.11 R12C12.1 59.25(n)
    59.11(a)
      174012  NM_062808.5  NP_495209.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GCV2(YMR189W)4
    GCV21
    P subunit of the mitochondrial glycine decarboxylase more4
    GCV21
    55.46(n)1
    54.75(a)1
      13(637500-640604)4
    8552271, 4  NP_013914.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons GLDP21 GLDP2 59.42(n)
    57.61(a)
      817149  NM_128167.3  NP_180178.1 
    rice
    (Oryza sativa)
    Liliopsida Os.266422 Oryza sativa (japonica cultivar-group) glycine dehydrogenase more 74.47(n)    AY346327.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for GLDC gene

    GLDC for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for GLDC
    PGOHUM00000245917


    (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 GLDC (see all 3600)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1219649761,2,,4
    C,FNon-ketotic hyperglycinemia (NKH)4 pathogenic16585992(-) AAGAGA/C/GACCAG 2 S R mis12NA EU 5870
    VAR_0168494
    Non-ketotic hyperglycinemia (NKH)4--see VAR_0168492 A P mis40--------
    VAR_0049794
    Non-ketotic hyperglycinemia (NKH)4--see VAR_0049792 S I mis40--------
    rs1219649771,2
    Cpathogenic16550183(-) CAGTGC/TGGCCC 2 A V mis10--------
    rs1219649801,2
    Cpathogenic16551531(-) CTGTCA/GCCCTG 2 H R mis10--------
    rs1219649741,2
    Cpathogenic16585179(-) GAACAG/TTTCGT 2 S I mis11Minor allele frequency- T:0.00NA 4550
    rs1219649791,2
    Cpathogenic16591871(-) CTTGGC/TGAATA 2 A V mis10--------
    rs1479392691,2
    C--6528812(+) GCCACC/TGCGCC 1 -- ds50010--------
    rs1401687831,2
    --6528814(+) CACCGC/TGCCTG 1 -- ds50010--------
    rs109756271,2
    C,F,H--6528843(+) TAATCC/GTAACT 1 -- ds500115Minor allele frequency- G:0.25NS EA NA CSA WA 1206

    HapMap Linkage Disequilibrium report for GLDC (6532464 - 6645692 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for GLDC (see all 15):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv416560CNV Insertion16902084
    nsv892164CNV Loss21882294
    nsv521556CNV Loss19592680
    nsv892166CNV Loss21882294
    dgv8023n71CNV Loss21882294
    nsv831498CNV Loss17160897
    dgv8022n71CNV Loss21882294
    nsv519777CNV Gain19592680
    esv2752308CNV Gain17911159
    nsv831497CNV Gain17160897

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

    (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: 238300   
    OMIM disorders: 605899  
    UniProtKB/Swiss-Prot: GCSP_HUMAN, P23378
  • Non-ketotic hyperglycinemia (NKH) [MIM:605899]: Autosomal recessive disease characterized by accumulation
    of a large amount of glycine in body fluid and by severe neurological symptoms. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 16 diseases for GLDC:    
    About MalaCards
    gldc-related glycine encephalopathy    infantile glycine encephalopathy    neonatal glycine encephalopathy    glycine encephalopathy
    atypical glycine encephalopathy    early myoclonic encephalopathy    autosomal recessive disease    neural tube defects
    tuberculosis    mental retardation    periodontitis    lung cancer
    hepatitis    multiple myeloma    myeloma    cerebritis

    2 diseases from the University of Copenhagen DISEASES database for GLDC:
    Glycine encephalopathy     Early myoclonic encephalopathy

    GLDC for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for GLDC gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hyperglycinemia nonketotic 95.5 12 10798358 (2), 15851735 (2), 16601880 (1), 2268343 (1) (see all 10)
    hyperglycinemia 94.9 5 1943691 (1), 12402263 (1), 15824356 (1), 18581728 (1)
    mental retardation 15.9 2 15824356 (1)
    tuberculosis 6.07 1 7698116 (1)
    shock 0 1 15295627 (1)

    GeneTests: GLDC
    GeneReviews: GLDC
    Genetic Association Database (GAD): GLDC
    Human Genome Epidemiology (HuGE) Navigator: GLDC (4 documents)

    Export disorders for GLDC 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 GLDC gene, integrated from 10 sources (see all 72):
    (articles sorted by number of sources associating them with GLDC)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures. (PubMed id 1993704)1, 2, 3, 9 Kume A.... Hiraga K. (J. Biol. Chem. 1991)
    2. Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia. (PubMed id 1996985)1, 2, 3, 9 Kure S.... Tada K. (Biochem. Biophys. Res. Commun. 1991)
    3. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PubMed id 16450403)1, 4, 9 Kure S....Matsubara Y. (Hum. Mutat. 2006)
    4. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. (PubMed id 17361008)1, 7, 9 Kanno J....Kure S. (J. Med. Genet. 2007)
    5. Recurrent mutations in P- and T-proteins of the glycine cleavage complex and a novel T-protein mutation (N145I): a strategy for the molecular investigation of patients with nonketotic hyperglycinemia (NKH). (PubMed id 11286506)1, 2, 9 Toone J.R.... James E.R. (Mol. Genet. Metab. 2001)
    6. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    7. Nonketotic hyperglycinemia (glycine encephalopathy): laboratory diagnosis. (PubMed id 11592811)1, 2 Applegarth D.A. and Toone J.R. (Mol. Genet. Metab. 2001)
    8. Identification of a common mutation in Finnish patients with nonketotic hyperglycinemia. (PubMed id 1634607)1, 2 Kure S.... Leisti J. (J. Clin. Invest. 1992)
    9. Human glycine decarboxylase gene (GLDC) and its highly conserved processed pseudogene (psiGLDC): their structure and expression, and the identification of a large deletion in a family with nonketotic hyperglycinemia. (PubMed id 10798358)1, 9 Takayanagi M....Narisawa K. (Hum. Genet. 2000)
    10. Mild glycine encephalopathy (NKH) in a large kindred due to a silent exonic GLDC splice mutation. (PubMed id 15851735)1, 9 Flusser H....Kure S. (Neurology 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
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      Query String
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    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: 2731 HGNC: 4313 AceView: GLDC Ensembl:ENSG00000178445 euGenes: HUgn2731
    ECgene: GLDC Kegg: 2731 H-InvDB: GLDC

    (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)
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    NameDescription
    PharmGKB entry for GLDC Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=GLDC[genesymbol]

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

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



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