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Aliases for GLDC Gene

Aliases for GLDC Gene

  • Glycine Dehydrogenase (Decarboxylating) 2 3
  • Glycine Decarboxylase 2 4 6
  • Glycine Dehydrogenase (Aminomethyl-Transferring) 3 4
  • Glycine Cleavage System Protein P 2 3
  • EC 1.4.4.2 4 63
  • 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 Protein P) 6
  • Glycine Cleavage System P Protein 4
  • Glycine Decarboxylase P-Protein 3
  • 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 Dehydrogenase (Decarboxylating)) is a Protein Coding gene. Diseases associated with GLDC include d-glycericacidemia and hyperglycinemia, isolated nonketotic. Among its related pathways are Metabolism and Glucose / Energy 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for GLDC Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for GLDC Gene at MOPED

Post-translational modifications for GLDC Gene

  • Ubiquitination at Lys447
  • Modification sites at PhosphoSitePlus

Other Protein References for GLDC Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains 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 :
  • P23378
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 --
GO:0009055 electron carrier activity TAS 2268343
GO:0016829 lyase activity IEA --
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with GLDC: view
genes like me logo Genes that share phenotypes with GLDC: view

Animal Model Products

CRISPR Products

miRNA for GLDC Gene

miRTarBase miRNAs that target GLDC

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for GLDC Gene

Localization for GLDC Gene

Subcellular locations from UniProtKB/Swiss-Prot for GLDC Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for GLDC Gene COMPARTMENTS Subcellular localization image for GLDC gene
Compartment Confidence
mitochondrion 5
chloroplast 2
cytosol 1
nucleus 1

Gene Ontology (GO) - Cellular Components for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with GLDC: view

Pathways for GLDC Gene

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

Pathways by source for GLDC Gene

1 Cell Signaling Technology pathway for GLDC Gene
2 BioSystems pathways for GLDC Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006520 cellular amino acid metabolic process --
GO:0006544 glycine metabolic process --
GO:0006546 glycine catabolic process IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with GLDC: view

Compounds for GLDC Gene

(7) HMDB Compounds for GLDC Gene

Compound Synonyms Cas Number PubMed IDs
Carbon dioxide
  • Carbon oxide
124-38-9
Glycine
  • 2-Aminoacetate
56-40-6
Lipoamide
  • Lipozyme
940-69-2
Methylamine
  • Aminomethane
74-89-5
Pyridoxal
  • 3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde
66-72-8

(2) Drugbank Compounds for GLDC Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Glycine
  • 2-Aminoacetic acid
56-40-6 target
Pyridoxal Phosphate
  • Codecarboxylase
54-47-7 target cofactor

(9) Novoseek inferred chemical compound relationships for GLDC Gene

Compound -log(P) Hits PubMed IDs
saci 66.7 2
dihydrolipoamide 63.5 1
alpha lipoic acid 61.3 1
tetrahydrofolate 60 1
polyglycolic acid 54.6 2
genes like me logo Genes that share compounds with GLDC: view

Transcripts for GLDC Gene

mRNA/cDNA for GLDC Gene

Unigene Clusters for GLDC Gene

Glycine dehydrogenase (decarboxylating):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for GLDC

Primer Products

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 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 (17.0) and Kidney - Cortex (7.9).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for GLDC Gene

SOURCE GeneReport for Unigene cluster for GLDC Gene Hs.584238

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

In Situ Assay Products

No data available for 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 35
  • 99.51 (n)
  • 99.51 (a)
GLDC 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia GLDC 35
  • 89.74 (n)
  • 93.73 (a)
GLDC 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GLDC 35
  • 90.33 (n)
  • 93.41 (a)
GLDC 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gldc 35
  • 86.94 (n)
  • 93.2 (a)
Gldc 16
Gldc 36
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GLDC 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 88 (a)
OneToMany
-- 36
  • 85 (a)
OneToMany
-- 36
  • 92 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Gldc 35
  • 87.04 (n)
  • 92.97 (a)
chicken
(Gallus gallus)
Aves GLDC 35
  • 77.7 (n)
  • 85.06 (a)
GLDC 36
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GLDC 36
  • 83 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia gldc-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia gldc 35
  • 76.33 (n)
  • 85.45 (a)
Str.8932 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3266 35
zebrafish
(Danio rerio)
Actinopterygii gldc 35
  • 71.55 (n)
  • 78.48 (a)
GLDC 36
  • 61 (a)
OneToOne
wufb23b05 35
fruit fly
(Drosophila melanogaster)
Insecta CG3999 35
  • 61.86 (n)
  • 64.56 (a)
CG3999 36
  • 63 (a)
OneToOne
CG3999 37
  • 64 (a)
worm
(Caenorhabditis elegans)
Secernentea R12C12.1 35
  • 59.25 (n)
  • 59.11 (a)
R12C12.1 36
  • 57 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV2 35
  • 55.46 (n)
  • 54.75 (a)
GCV2 36
  • 50 (a)
OneToOne
GCV2 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12738g 35
  • 56.42 (n)
  • 57.49 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6847 35
soybean
(Glycine max)
eudicotyledons Gma.15027 35
thale cress
(Arabidopsis thaliana)
eudicotyledons GLDP2 35
  • 59.42 (n)
  • 57.61 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.2570 35
corn
(Zea mays)
Liliopsida Zm.1072 35
rice
(Oryza sativa)
Liliopsida Os.26642 35
Os01g0711400 35
  • 58.29 (n)
  • 56.98 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.26552 35
bread mold
(Neurospora crassa)
Ascomycetes NCU02475 35
  • 54.84 (n)
  • 55.51 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv2 35
  • 55.01 (n)
  • 53.39 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13341 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 61 (a)
OneToOne
Species with no ortholog for GLDC:
  • 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 MAF
rs928393 -- 6,542,674(-) tcctg(A/G)gctca intron-variant
rs934854 -- 6,631,611(+) TTGAA(A/G)TGAGA intron-variant
rs934855 -- 6,631,702(+) AGAAG(G/T)GAAGA intron-variant
rs968196 -- 6,586,788(+) aggtt(C/G)ggcca intron-variant
rs968197 -- 6,587,054(+) ACAAA(A/T)AAGTT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv831497 CNV Gain 17160897
nsv892162 CNV Gain 21882294
nsv831498 CNV Loss 17160897
nsv892163 CNV Gain 21882294
esv2752308 CNV Gain 17911159
nsv892164 CNV Loss 21882294
nsv466111 CNV Gain 19166990
dgv2278e1 CNV Complex 17122850
nsv892165 CNV Gain 21882294
nsv892166 CNV Loss 21882294
nsv519777 CNV Gain 19592680
nsv416560 CNV Insertion 16902084
nsv521556 CNV Loss 19592680
dgv8022n71 CNV Loss 21882294
dgv8023n71 CNV Loss 21882294

Relevant External Links for GLDC Gene

HapMap Linkage Disequilibrium report
GLDC
Human Gene Mutation Database (HGMD)
GLDC

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

Disorders for GLDC Gene

(1) OMIM Diseases for GLDC Gene (238300)

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.

(2) University of Copenhagen DISEASES for GLDC Gene

(5) Novoseek inferred disease relationships for GLDC Gene

Disease -log(P) Hits PubMed IDs
hyperglycinemia nonketotic 95.5 12
hyperglycinemia 94.9 4
mental retardation 15.9 1
tuberculosis 6.07 1
shock 0 1

Relevant External Links for GLDC

GeneTests
GLDC
GeneReviews
GLDC
Genetic Association Database (GAD)
GLDC
Human Genome Epidemiology (HuGE) Navigator
GLDC
genes like me logo Genes that share disorders with GLDC: view

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 23
  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 23
  3. 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 23
  4. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S. … Matsubara Y. (Hum. Mutat. 2006) 3 23 48
  5. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. (PMID: 17361008) Kanno J. … Kure S. (J. Med. Genet. 2007) 3 23 25

Products for GLDC Gene

Sources for GLDC Gene

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