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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 Cleavage System Protein P 2 3
  • 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
  • EC 4
  • 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 Metabolism and Glyoxylate metabolism and glycine degradation. Gene Ontology (GO) annotations related to this gene include electron transfer 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

GeneHancer (GH) Regulatory Elements for GLDC Gene

Promoters and enhancers for GLDC Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J006644 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 681.2 -0.1 -98 3.4 HDGF ARID4B SIN3A ZNF48 YY1 GTF3C2 SLC30A9 ZNF213 ZNF143 ATF7 GLDC ENSG00000236924 UHRF2 AK4P4 RNF2P1
GH09J006564 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.2 +79.1 79103 4.6 NFIB BATF RAD21 RCOR1 FOS ETV6 ZNF654 JUNB CEBPB SP1 GLDC RPL35AP20 ENSG00000237158 RN7SL25P
GH09J006590 Enhancer 0.9 ENCODE 42.3 +54.2 54211 2.2 FOXA2 MLX ARID4B DMAP1 ETS1 SP5 MXD4 PPARG KAT8 NFIL3 GLDC ENSG00000237158 ENSG00000236924 KDM4C GC09M006597
GH09J006703 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 16.2 -58.3 -58337 1.7 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A IRF4 YY1 GLIS2 ZNF207 LOC105375968 KDM4C GLDC ENSG00000236924 ENSG00000225489 SNRPEP2 GC09P006678
GH09J006632 Enhancer 0.8 ENCODE 33.7 +13.0 12953 1.2 HDGF SOX13 SAP130 ARID4B BATF IRF4 THRB TEAD3 POLR2A NFATC1 GLDC PIR41771 RPL23AP57
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GLDC on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GLDC gene promoter:
  • AREB6
  • MyoD
  • Pax-2b
  • Pax-2a
  • Pax-2
  • C/EBPalpha
  • CUTL1
  • Pax-5
  • Lhx3a
  • LHX3b

Genomic Locations for GLDC Gene

Genomic Locations for GLDC Gene
113,320 bases
Minus strand
113,229 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

Post-translational modifications for GLDC Gene

  • Ubiquitination at isoforms=447
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GLDC Gene

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

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).
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).
GENATLAS Biochemistry:
glycine decarboxylase pyridoxal-phosphate dependent 120kDa,P protein,catalyzing the first step of the glycine cleavage system

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 transfer 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 Gldc<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for GLDC Gene

miRTarBase miRNAs that target GLDC

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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:0005829 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,IDA 28244183
GO:0019464 glycine decarboxylation via glycine cleavage system IEA --
GO:0022900 electron transport chain IEA --
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 254
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Citalopram Approved Pharma 526
Escitalopram Approved, Investigational Pharma 0
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 1,2-Dithiolane-3-pentanamide
  • alpha-Lipoic acid amide
  • Lipoacin
  • Thioctamide
  • Thioctic acid amide
  • 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

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(107) Selected AceView cDNA sequences:
(22) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GLDC Gene

Glycine dehydrogenase (decarboxylating):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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, 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 34 33
  • 99.51 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
-- 34
  • 88 (a)
-- 34
  • 85 (a)
(Canis familiaris)
Mammalia GLDC 34 33
  • 90.33 (n)
(Bos Taurus)
Mammalia GLDC 34 33
  • 89.74 (n)
(Rattus norvegicus)
Mammalia Gldc 33
  • 87.04 (n)
(Monodelphis domestica)
Mammalia GLDC 34
  • 87 (a)
(Mus musculus)
Mammalia Gldc 16 34 33
  • 86.94 (n)
(Gallus gallus)
Aves GLDC 34 33
  • 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 34 35 33
  • 61.86 (n)
(Caenorhabditis elegans)
Secernentea R12C12.1 34 33
  • 59.25 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12738g 33
  • 56.42 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV2 36 34 33
  • 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
(Zea mays)
Liliopsida Zm.1072 33
(Triticum aestivum)
Liliopsida Ta.26552 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
Cin.13341 33
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)
Evolutionary constrained regions (ECRs) for GLDC: view image

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 Variation AA Info Type
rs1039584725 uncertain-significance, Non-ketotic hyperglycinemia 6,645,672(-) A/C 5_prime_UTR_variant
rs1057515605 uncertain-significance, Non-ketotic hyperglycinemia 6,533,133(-) A/G coding_sequence_variant, missense_variant
rs1057515606 uncertain-significance, Non-ketotic hyperglycinemia 6,540,066(-) T/C coding_sequence_variant, missense_variant
rs1057515607 uncertain-significance, Non-ketotic hyperglycinemia 6,592,895(-) C/A coding_sequence_variant, missense_variant
rs1057515608 uncertain-significance, Non-ketotic hyperglycinemia 6,645,358(-) C/A coding_sequence_variant, missense_variant

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

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

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)

Additional Variant Information for GLDC Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for GLDC Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
glycine encephalopathy
  • gce
neonatal glycine encephalopathy
  • classic glycine encephalopathy
glycine encephalopathy with normal serum glycine
  • atypical glycine encephalopathy
infantile glycine encephalopathy
  • infantile nkh
epilepsy, idiopathic generalized
  • eig
- 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, ECO:0000269 PubMed:28737873}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GLDC

Genetic Association Database
Human Genome Epidemiology 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 58
  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 58
  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 58
  4. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S … Matsubara Y (Human mutation 2006) 3 22 44 58
  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 58

Products for GLDC Gene

Sources for GLDC Gene

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