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Aliases for GLDC Gene

Aliases for GLDC Gene

  • Glycine Decarboxylase 2 3 4 5
  • Glycine Dehydrogenase (Aminomethyl-Transferring) 3 4
  • Glycine Dehydrogenase (Decarboxylating) 2 3
  • Glycine Cleavage System Protein P 2 3
  • EC 1.4.4.2 4 61
  • GCSP 3 4
  • Glycine Dehydrogenase (Decarboxylating; Glycine Decarboxylase, Glycine Cleavage System Protein P) 2
  • Glycine Dehydrogenase (Decarboxylating), Mitochondrial 3
  • Glycine Dehydrogenase [Decarboxylating], Mitochondrial 3
  • Glycine Cleavage System P Protein 4
  • Glycine Decarboxylase P-Protein 3
  • Glycine Dehydrogenase 2
  • HYGN1 3
  • GCE 3

External Ids for GLDC Gene

Previous GeneCards Identifiers for GLDC Gene

  • GC09M006686
  • GC09M006513

Summaries for GLDC Gene

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 Decarboxylase) is a Protein Coding gene. Diseases associated with GLDC include Glycine Encephalopathy and Neonatal Glycine Encephalopathy. Among its related pathways are Glycine, serine and threonine metabolism and Metabolism. GO annotations related to this gene include electron carrier activity and lyase activity.

UniProtKB/Swiss-Prot for GLDC Gene

  • The glycine cleavage system catalyzes the degradation of glycine. The P protein (GLDC) 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 (GCSH).

Gene Wiki entry for GLDC Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GLDC Gene

Genomics for GLDC Gene

Regulatory Elements for GLDC Gene

Enhancers for GLDC Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09F006590 0.9 ENCODE 42.3 +54.1 54121 2.2 ELF3 ATF1 MLX ARID4B DMAP1 RAD21 ZSCAN9 DNMT3B RARA GATA4 GLDC ENSG00000237158 ENSG00000236924 KDM4C GC09M006597
GH09F006632 1 Ensembl ENCODE 33.6 +12.9 12863 1.2 HDGF SOX13 MXI1 SAP130 ARID4B THRB TEAD3 POLR2A EGR1 EED GLDC PIR41771 RPL23AP57
GH09F006644 1 ENCODE 31.2 +0.1 87 2.9 HDGF ARID4B SIN3A ZNF48 YY1 GTF3C2 SLC30A9 ZNF143 ZNF263 SP3 GLDC AK4P4 RNF2P1 RPL23AP57
GH09F006551 1.1 FANTOM5 Ensembl ENCODE 15.3 +92.8 92793 3.1 CTCF ZNF664 POLR2A NFIA GLIS1 JUN GLDC ENSG00000233367 KDM4C ENSG00000236924 RN7SL25P ENSG00000237158
GH09F006603 0.4 FANTOM5 42 +42.1 42104 0.2 EGR2 GLDC ENSG00000236924 KDM4C GC09M006597 PIR47562
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GLDC on UCSC Golden Path with GeneCards custom track

Promoters for GLDC Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001299758 191 3000 HDGF ARID4B SIN3A ZNF48 YY1 GTF3C2 SLC30A9 ZNF143 ZNF263 SP3

Genomic Location for GLDC Gene

Chromosome:
9
Start:
6,532,464 bp from pter
End:
6,645,692 bp from pter
Size:
113,229 bases
Orientation:
Minus strand

Genomic View for GLDC Gene

Genes around GLDC on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GLDC Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GLDC Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GLDC Gene

Proteins for GLDC Gene

  • Protein details for GLDC Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P23378-GCSP_HUMAN
    Recommended name:
    Glycine dehydrogenase (decarboxylating), mitochondrial
    Protein Accession:
    P23378
    Secondary Accessions:
    • Q2M2F8

    Protein attributes for GLDC Gene

    Size:
    1020 amino acids
    Molecular mass:
    112730 Da
    Cofactor:
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Interacts with GCSH (By similarity). Homodimer. The glycine cleavage system is composed of four proteins: P (GLDC), T (GCST), L (DLD) and H (GCSH).

neXtProt entry for GLDC Gene

Selected DME Specific Peptides for GLDC Gene

P23378:
  • GGQVYLDGAN
  • WDRPYSR
  • PLDQAQGY
  • DGANMNA
  • HQHGGQVY
  • GPIGVKK
  • KAELDRF
  • SILPISW
  • ANASLLDE
  • ATETAILNANY
  • AHGTNPASA
  • CTAQALLA
  • PHGGGGPG
  • GGPHAAF
  • DYGFHAP
  • GSSQRFG
  • QPNSGAQGEY
  • GYGGPHAA
  • SAHGTNPA
  • LVCTCPP
  • QGRLESLLN
  • QTREQHIR
  • MITYPST
  • RYMKKLEN
  • THQVFNS
  • YTPYQPE
  • ELDRFCDA
  • PTMSWPV
  • ATDLLAL
  • REQHIRR
  • PLGSCTMK
  • ALQTREQHI
  • KATSNICT
  • HLNLHKTF
  • SYIGMGY
  • GTLMVEPTESE

Post-translational modifications for GLDC Gene

  • Ubiquitination at Lys 447
  • Modification sites at PhosphoSitePlus

Other Protein References for GLDC Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for GLDC (GLDC)

Domains & Families for GLDC Gene

Suggested Antigen Peptide Sequences for GLDC Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P23378

UniProtKB/Swiss-Prot:

GCSP_HUMAN :
  • Belongs to the GcvP family.
Family:
  • Belongs to the GcvP family.
genes like me logo Genes that share domains with GLDC: view

No data available for Gene Families for GLDC Gene

Function for GLDC Gene

Molecular function for GLDC Gene

GENATLAS Biochemistry:
glycine decarboxylase pyridoxal-phosphate dependent 120kDa,P protein,catalyzing the first step of the glycine cleavage system
UniProtKB/Swiss-Prot CatalyticActivity:
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).
UniProtKB/Swiss-Prot EnzymeRegulation:
Stimulated by lipoic acid. Inhibited in presence of methylamine (By similarity).
UniProtKB/Swiss-Prot Function:
The glycine cleavage system catalyzes the degradation of glycine. The P protein (GLDC) 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 (GCSH).

Enzyme Numbers (IUBMB) for GLDC Gene

Gene Ontology (GO) - Molecular Function for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004375 glycine dehydrogenase (decarboxylating) activity IEA,TAS --
GO:0009055 electron carrier activity TAS 2268343
GO:0016491 oxidoreductase activity IEA --
GO:0016594 glycine binding IBA --
GO:0016829 lyase activity IEA --
genes like me logo Genes that share ontologies with GLDC: view
genes like me logo Genes that share phenotypes with GLDC: view

Human Phenotype Ontology for GLDC Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GLDC Gene

MGI Knock Outs for GLDC:
  • Gldc tm1a(EUCOMM)Wtsi

Animal Model Products

miRNA for GLDC Gene

miRTarBase miRNAs that target GLDC

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for GLDC

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for GLDC Gene

Localization for GLDC Gene

Subcellular locations from UniProtKB/Swiss-Prot for GLDC Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GLDC gene
Compartment Confidence
mitochondrion 5
nucleus 5
plasma membrane 4
cytosol 1

Gene Ontology (GO) - Cellular Components for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005739 mitochondrion IDA,IBA --
GO:0005759 mitochondrial matrix TAS --
GO:0005829 NOT cytosol IBA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with GLDC: view

Pathways & Interactions for GLDC Gene

genes like me logo Genes that share pathways with GLDC: view

Pathways by source for GLDC Gene

Gene Ontology (GO) - Biological Process for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006520 cellular amino acid metabolic process IEA --
GO:0006544 glycine metabolic process IEA --
GO:0006546 glycine catabolic process IEA,TAS 1996985
GO:0019464 glycine decarboxylation via glycine cleavage system IBA --
GO:0046487 glyoxylate metabolic process TAS --
genes like me logo Genes that share ontologies with GLDC: view

No data available for SIGNOR curated interactions for GLDC Gene

Drugs & Compounds for GLDC Gene

(8) Drugs for GLDC Gene - From: DrugBank, PharmGKB, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 226
Citalopram Approved Pharma 503
Escitalopram Approved, Investigational Pharma 0
Carbon dioxide Approved, Vet_approved Pharma 0
Pyridoxal Approved Nutra 185

(10) Additional Compounds for GLDC Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Lipoamide
  • 1,2-Dithiolane-3-pentanamide
  • 5-(1,2-Dithiolan-3-yl)-pentanamide
  • 5-(1,2-Dithiolan-3-yl)pentanamide
  • 5-(1,2-Dithiolan-3-yl)valeramide
  • 5-(Dithiolan-3-yl)valeramide
940-69-2
S-aminomethyldihydrolipoamide
  • 8-[(Aminomethyl)sulfanyl]-6-sulfanyloctanamide
genes like me logo Genes that share compounds with GLDC: view

Transcripts for GLDC Gene

Unigene Clusters for GLDC Gene

Glycine dehydrogenase (decarboxylating):
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for GLDC

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for GLDC Gene

No ASD Table

Relevant External Links for GLDC Gene

GeneLoc Exon Structure for
GLDC
ECgene alternative splicing isoforms for
GLDC

Expression for GLDC Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GLDC Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GLDC Gene

This gene is overexpressed in Liver (x17.0) and Kidney - Cortex (x7.9).

Protein differential expression in normal tissues from HIPED for GLDC Gene

This gene is overexpressed in Liver (46.4) and Fetal Liver (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GLDC Gene



NURSA nuclear receptor signaling pathways regulating expression of GLDC Gene:

GLDC

SOURCE GeneReport for Unigene cluster for GLDC Gene:

Hs.584238
genes like me logo Genes that share expression patterns with GLDC: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for GLDC Gene

Orthologs for GLDC Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GLDC Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GLDC 34 35
  • 99.51 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 92 (a)
OneToMany
-- 35
  • 88 (a)
OneToMany
-- 35
  • 85 (a)
OneToMany
dog
(Canis familiaris)
Mammalia GLDC 34 35
  • 90.33 (n)
cow
(Bos Taurus)
Mammalia GLDC 34 35
  • 89.74 (n)
rat
(Rattus norvegicus)
Mammalia Gldc 34
  • 87.04 (n)
oppossum
(Monodelphis domestica)
Mammalia GLDC 35
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gldc 34 16 35
  • 86.94 (n)
chicken
(Gallus gallus)
Aves GLDC 34 35
  • 77.7 (n)
lizard
(Anolis carolinensis)
Reptilia GLDC 35
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gldc 34
  • 76.33 (n)
Str.8932 34
African clawed frog
(Xenopus laevis)
Amphibia gldc-prov 34
zebrafish
(Danio rerio)
Actinopterygii gldc 34
  • 71.55 (n)
GLDC 35
  • 61 (a)
OneToOne
wufb23b05 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3266 34
fruit fly
(Drosophila melanogaster)
Insecta CG3999 36 34 35
  • 61.86 (n)
worm
(Caenorhabditis elegans)
Secernentea R12C12.1 34 35
  • 59.25 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12738g 34
  • 56.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV2 34 35 37
  • 55.46 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons GLDP2 34
  • 59.42 (n)
soybean
(Glycine max)
eudicotyledons Gma.15027 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6847 34
rice
(Oryza sativa)
Liliopsida Os01g0711400 34
  • 58.29 (n)
Os.26642 34
barley
(Hordeum vulgare)
Liliopsida Hv.2570 34
wheat
(Triticum aestivum)
Liliopsida Ta.26552 34
corn
(Zea mays)
Liliopsida Zm.1072 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 61 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv2 34
  • 55.01 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02475 34
  • 54.84 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13341 34
Species where no ortholog for GLDC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for GLDC Gene

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

Paralogs for GLDC Gene

Pseudogenes.org Pseudogenes for GLDC Gene

genes like me logo Genes that share paralogs with GLDC: view

No data available for Paralogs for GLDC Gene

Variants for GLDC Gene

Sequence variations from dbSNP and Humsavar for GLDC Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs121964974 Non-ketotic hyperglycinemia (NKH) [MIM:605899], Pathogenic 6,588,417(-) GAACA(G/T)TTCGT reference, missense
rs121964976 Non-ketotic hyperglycinemia (NKH) [MIM:605899], Pathogenic 6,589,230(-) AAGAG(A/G)ACCAG reference, synonymous-codon
rs386833589 Non-ketotic hyperglycinemia (NKH) [MIM:605899], Likely pathogenic 6,605,145(-) AGAGA(C/G)CTCAT reference, missense
rs121964977 Pathogenic 6,553,420(-) CAGTG(C/T)GGCCC reference, missense
rs121964978 Pathogenic 6,645,498(-) GGCCA(C/T)GCAGT reference, missense

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

Variant ID Type Subtype PubMed ID
nsv972293 CNV duplication 23825009
nsv831498 CNV loss 17160897
nsv831497 CNV gain 17160897
nsv613208 CNV gain 21841781
nsv613207 CNV loss 21841781
nsv613206 CNV loss 21841781
nsv521556 CNV loss 19592680
nsv519777 CNV gain 19592680
nsv466111 CNV gain 19166990
nsv416560 CNV insertion 16902084
nsv1161829 CNV deletion 26073780
nsv1033539 CNV gain 25217958
nsv1033268 CNV loss 25217958
nsv1029665 CNV gain 25217958
nsv1025627 CNV loss 25217958
nsv1023706 CNV gain 25217958
nsv1018845 CNV gain 25217958
nsv1016600 CNV gain 25217958
esv3619411 CNV gain 21293372
esv3619410 CNV gain 21293372
esv3619407 CNV gain 21293372
esv3619406 CNV gain 21293372
esv3576621 CNV gain 25503493
esv3573096 CNV loss 25503493
esv3544471 CNV deletion 23714750
esv2764163 CNV loss 21179565
esv2761298 CNV gain 21179565
esv2759661 CNV loss 17122850
esv2752308 CNV gain 17911159
dgv7389n100 CNV loss 25217958
dgv7388n100 CNV gain 25217958
dgv7386n100 CNV gain 25217958
dgv12488n54 CNV gain 21841781

Variation tolerance for GLDC Gene

Residual Variation Intolerance Score: 29.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.35; 76.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GLDC Gene

Human Gene Mutation Database (HGMD)
GLDC
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GLDC

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

Disorders for GLDC Gene

MalaCards: The human disease database

(8) MalaCards diseases for GLDC Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
glycine encephalopathy
  • non-ketotic hyperglycinemia
neonatal glycine encephalopathy
  • classic glycine encephalopathy
infantile glycine encephalopathy
  • infantile nkh
d-glycericacidemia
  • d-glycerate kinase deficiency
atypical glycine encephalopathy
  • atypical nka
- elite association - COSMIC cancer census association via MalaCards
Search GLDC in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GCSP_HUMAN
  • 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. {ECO:0000269 PubMed:11286506, ECO:0000269 PubMed:11592811, ECO:0000269 PubMed:1634607, ECO:0000269 PubMed:1996985}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for GLDC

Genetic Association Database (GAD)
GLDC
Human Genome Epidemiology (HuGE) Navigator
GLDC
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GLDC
genes like me logo Genes that share disorders with GLDC: view

No data available for Genatlas for GLDC Gene

Publications for GLDC Gene

  1. The glycine cleavage system. Molecular cloning of the chicken and human glycine decarboxylase cDNAs and some characteristics involved in the deduced protein structures. (PMID: 1993704) Kume A. … Hiraga K. (J. Biol. Chem. 1991) 2 3 4 22 64
  2. Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia. (PMID: 1996985) Kure S. … Tada K. (Biochem. Biophys. Res. Commun. 1991) 2 3 4 22 64
  3. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. (PMID: 17361008) Kanno J. … Kure S. (J. Med. Genet. 2007) 3 22 25 64
  4. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S. … Matsubara Y. (Hum. Mutat. 2006) 3 22 46 64
  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). (PMID: 11286506) Toone J.R. … James E.R. (Mol. Genet. Metab. 2001) 3 4 22 64

Products for GLDC Gene

Sources for GLDC Gene

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