Free for academic non-profit institutions. Other users need a Commercial license

Aliases for GLDC Gene

Aliases for GLDC Gene

  • Glycine Decarboxylase 2 3 4 5
  • Glycine Dehydrogenase (Aminomethyl-Transferring) 3 4
  • Glycine Cleavage System Protein P 2 3
  • EC 4 58
  • 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 Dehydrogenase (Decarboxylating) 2
  • 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 D-Glycericacidemia. Among its related pathways are Metabolism and Glyoxylate metabolism and glycine degradation. 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

Additional gene information for GLDC Gene

No data available for CIViC summary , 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
GH09H006590 0.9 ENCODE 42.3 +54.2 54212 2.2 ELF3 FOXA2 ATF1 MLX ARID4B DMAP1 RAD21 DNMT3B ZSCAN9 RARA GLDC ENSG00000237158 ENSG00000236924 KDM4C GC09M006597
GH09H006644 1.2 Ensembl ENCODE 31.1 -0.1 -98 3.4 HDGF ARID4B SIN3A YY1 GTF3C2 SLC30A9 ZNF143 ATF7 RUNX3 SP3 GLDC UHRF2 AK4P4 RNF2P1 ENSG00000236924
GH09H006632 0.8 ENCODE 33.7 +13.0 12954 1.2 HDGF SOX13 SAP130 MAX ARID4B BATF THRB TEAD3 POLR2A EED GLDC PIR41771 RPL23AP57
GH09H006703 1.3 ENCODE dbSUPER 16.2 -58.3 -58338 1.7 HDGF PKNOX1 ARID4B SIN3A YY1 GLIS2 ZNF143 ZNF207 FOS ATF7 GLDC ENSG00000236924 ENSG00000225489 SNRPEP2 LOC105375968 GC09P006678
GH09H006690 1.1 Ensembl ENCODE dbSUPER 18.2 -44.8 -44845 0.7 TBL1XR1 NR2F1 ELF1 ATF2 RELA ZNF217 BCL11A ATF7 IKZF2 SPI1 GLDC KDM4C ENSG00000236924 LOC105375968 GC09P006678
- 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
ENSR00000232958 -217 1200 HDGF ARID4B SIN3A YY1 GTF3C2 SLC30A9 ZNF143 ATF7 RUNX3 SP3

Genomic Locations for GLDC Gene

Genomic Locations for GLDC Gene
113,320 bases
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:
    Recommended name:
    Glycine dehydrogenase (decarboxylating), mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q2M2F8

    Protein attributes for GLDC Gene

    1020 amino acids
    Molecular mass:
    112730 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer (By similarity). Interacts with GCSH (By similarity). 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


Post-translational modifications for GLDC Gene

  • Ubiquitination at isoforms=447
  • Modification sites at PhosphoSitePlus

Antibody Products

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

Domains & Families for GLDC Gene

Gene Families for GLDC Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for GLDC Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



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

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

Phenotypes From GWAS Catalog 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 IEA --
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

CRISPR Products

miRNA for GLDC Gene

miRTarBase miRNAs that target GLDC

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for GLDC

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


Subcellular locations from

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GLDC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005739 mitochondrion IDA,IEA 28244183
GO:0005759 mitochondrial matrix TAS --
GO:0005886 plasma membrane IDA --
GO:0005960 glycine cleavage complex IEA --
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 IDA,IEA 28244183
GO:0019464 glycine decarboxylation via glycine cleavage system IEA --
GO:0036255 response to methylamine ISS --
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 243
Citalopram Approved Pharma 520
Escitalopram Approved, Investigational Pharma 0
Carbon dioxide Approved, Vet_approved Pharma 0
Pyridoxal Approved Nutra 192

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 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
  • 8-[(Aminomethyl)sulfanyl]-6-sulfanyloctanamide
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

Clone Products

  • Addgene plasmids for GLDC

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

No ASD Table

Relevant External Links for GLDC Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GLDC Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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:


SOURCE GeneReport for Unigene cluster for GLDC Gene:


Evidence on tissue expression from TISSUES for GLDC Gene

  • Liver(4.6)
  • Nervous system(4.5)
  • Blood(4.2)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GLDC Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • nervous
  • respiratory
  • skeletal muscle
Head and neck:
  • brain
  • epiglottis
  • head
  • neck
  • diaphragm
  • lung
  • spinal cord
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
(Pan troglodytes)
Mammalia GLDC 33 34
  • 99.51 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
-- 34
  • 88 (a)
-- 34
  • 85 (a)
(Canis familiaris)
Mammalia GLDC 33 34
  • 90.33 (n)
(Bos Taurus)
Mammalia GLDC 33 34
  • 89.74 (n)
(Rattus norvegicus)
Mammalia Gldc 33
  • 87.04 (n)
(Monodelphis domestica)
Mammalia GLDC 34
  • 87 (a)
(Mus musculus)
Mammalia Gldc 33 16 34
  • 86.94 (n)
(Gallus gallus)
Aves GLDC 33 34
  • 77.7 (n)
(Anolis carolinensis)
Reptilia GLDC 34
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia gldc 33
  • 76.33 (n)
Str.8932 33
African clawed frog
(Xenopus laevis)
Amphibia gldc-prov 33
(Danio rerio)
Actinopterygii gldc 33
  • 71.55 (n)
  • 61 (a)
wufb23b05 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3266 33
fruit fly
(Drosophila melanogaster)
Insecta CG3999 35 33 34
  • 61.86 (n)
(Caenorhabditis elegans)
Secernentea R12C12.1 33 34
  • 59.25 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12738g 33
  • 56.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV2 33 34 36
  • 55.46 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons GLDP2 33
  • 59.42 (n)
(Glycine max)
eudicotyledons Gma.15027 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6847 33
(Oryza sativa)
Liliopsida Os01g0711400 33
  • 58.29 (n)
Os.26642 33
(Hordeum vulgare)
Liliopsida Hv.2570 33
(Triticum aestivum)
Liliopsida Ta.26552 33
(Zea mays)
Liliopsida Zm.1072 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv2 33
  • 55.01 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02475 33
  • 54.84 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13341 33
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

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

Paralogs for GLDC Gene 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
rs10975674 Non-ketotic hyperglycinemia (NKH) [MIM:605899] 6,602,180(+) AAGAC(A/G)ATACA reference, missense
rs121964974 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 6,588,417(-) GAACA(G/T)TTCGT reference, missense
rs121964976 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 6,589,230(-) AAGAG(A/C/G)ACCAG reference, synonymous-codon, missense
rs150171524 Non-ketotic hyperglycinemia (NKH) [MIM:605899] 6,602,147(+) TCTCC(A/G)AATGT reference, missense
rs188269735 Non-ketotic hyperglycinemia (NKH) [MIM:605899] 6,536,188(+) GCTCC(A/C)CCATG 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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for GLDC Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
glycine encephalopathy
  • non-ketotic hyperglycinemia
  • d-glycerate kinase deficiency
neonatal glycine encephalopathy
  • classic glycine encephalopathy
idiopathic generalized epilepsy
  • generalised epilepsy
glycine encephalopathy with normal serum glycine
  • atypical glycine encephalopathy
- elite association - COSMIC cancer census association via MalaCards
Search GLDC in MalaCards View complete list of genes associated with diseases


  • 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, ECO:0000269 PubMed:28244183}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for GLDC

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 (The Journal of biological chemistry 1991) 2 3 4 22 60
  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 (Biochemical and biophysical research communications 1991) 2 3 4 22 60
  3. Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia. (PMID: 17361008) Kanno J … Kure S (Journal of medical genetics 2007) 3 22 25 60
  4. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S … Matsubara Y (Human mutation 2006) 3 22 45 60
  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 JR … James ER (Molecular genetics and metabolism 2001) 3 4 22 60

Products for GLDC Gene

Sources for GLDC Gene

Loading form....