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Aliases for GLDC Gene

Aliases for GLDC Gene

  • Glycine Dehydrogenase (Decarboxylating) 2 3
  • Glycine Dehydrogenase (Aminomethyl-Transferring) 3 4
  • Glycine Cleavage System Protein P 2 3
  • Glycine Decarboxylase 2 4
  • 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 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 glycine encephalopathy and gldc-related glycine encephalopathy. Among its related pathways are Metabolism and Carbon 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

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

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 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 TAS --
GO:0009055 electron carrier activity TAS 2268343
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

Animal Model Products

miRNA for GLDC Gene

miRTarBase miRNAs that target GLDC

No data available for Animal Models , 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
Jensen Localization Image for GLDC Gene COMPARTMENTS Subcellular localization image for GLDC gene
Compartment Confidence
mitochondrion 5
chloroplast 1

Gene Ontology (GO) - Cellular Components for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IBA --
GO:0005759 mitochondrial matrix TAS --
GO:0005829 NOT cytosol IBA --
GO:0005960 glycine cleavage complex IBA --
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

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 TAS 1996985
GO:0019464 glycine decarboxylation via glycine cleavage system IBA --
GO:0034641 cellular nitrogen compound 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

(7) Drugs for GLDC Gene - From: HMDB, DrugBank, PharmGKB, and NovoSeek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved Nutra Agonist, Target Endogenous potentiator, co-transmitter 102
Citalopram Approved Pharma 485
Escitalopram Approved, Investigational Pharma 0
Pyridoxal Approved Nutra 150
Methylamine Experimental Pharma 0

(11) Additional Compounds for GLDC Gene - From: HMDB and NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
124-38-9
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
ALPHA LIPOIC ACID
Carbon
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:

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 (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, MOPED, and MaxQB for GLDC Gene



SOURCE GeneReport for Unigene cluster for GLDC Gene Hs.584238

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

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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
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
chimpanzee
(Pan troglodytes)
Mammalia GLDC 35
  • 99.51 (n)
  • 99.51 (a)
GLDC 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gldc 35
  • 87.04 (n)
  • 92.97 (a)
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
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
tropical clawed frog
(Silurana tropicalis)
Amphibia gldc 35
  • 76.33 (n)
  • 85.45 (a)
Str.8932 35
African clawed frog
(Xenopus laevis)
Amphibia gldc-prov 35
zebrafish
(Danio rerio)
Actinopterygii gldc 35
  • 71.55 (n)
  • 78.48 (a)
wufb23b05 35
GLDC 36
  • 61 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3266 35
fruit fly
(Drosophila melanogaster)
Insecta CG3999 37
  • 64 (a)
CG3999 35
  • 61.86 (n)
  • 64.56 (a)
CG3999 36
  • 63 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea R12C12.1 35
  • 59.25 (n)
  • 59.11 (a)
R12C12.1 36
  • 57 (a)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12738g 35
  • 56.42 (n)
  • 57.49 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV2 35
  • 55.46 (n)
  • 54.75 (a)
GCV2 36
  • 50 (a)
OneToOne
GCV2 38
thale cress
(Arabidopsis thaliana)
eudicotyledons GLDP2 35
  • 59.42 (n)
  • 57.61 (a)
soybean
(Glycine max)
eudicotyledons Gma.15027 35
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6847 35
barley
(Hordeum vulgare)
Liliopsida Hv.2570 35
rice
(Oryza sativa)
Liliopsida Os.26642 35
Os01g0711400 35
  • 58.29 (n)
  • 56.98 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.26552 35
corn
(Zea mays)
Liliopsida Zm.1072 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13341 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 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/T)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

Variation tolerance for GLDC Gene

Residual Variation Intolerance Score: 29.71% 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

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

MalaCards: The human disease database

(6) 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
gldc-related glycine encephalopathy
d-glycericacidemia
  • d-glycerate kinase deficiency
atypical glycine encephalopathy
  • atypical nka
neonatal glycine encephalopathy
  • classic glycine encephalopathy
- elite association
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. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. (PMID: 17361008) Kanno J. … Kure S. (J. Med. Genet. 2007) 23 25 26 67
  2. 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 23 67
  3. 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 23 67
  4. A mathematical model gives insights into the effects of vitamin B-6 deficiency on 1-carbon and glutathione metabolism. (PMID: 19244383) Nijhout H.F. … Reed M.C. (J. Nutr. 2009) 23 67
  5. The role of the mitochondrial glycine cleavage complex in the metabolism and virulence of the protozoan parasite Leishmania major. (PMID: 17981801) Scott D.A. … Beverley S.M. (J. Biol. Chem. 2008) 23 67

Products for GLDC Gene

Sources for GLDC Gene

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