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Aliases for GCSH Gene

Aliases for GCSH Gene

  • Glycine Cleavage System Protein H 2 3 5
  • Lipoic Acid-Containing Protein 2 3 4
  • Glycine Cleavage System Protein H (Aminomethyl Carrier) 2 3
  • Glycine Cleavage System H Protein, Mitochondrial 3
  • Mitochondrial Glycine Cleavage System H-Protein 3
  • GCE 3
  • NKH 3

External Ids for GCSH Gene

Previous GeneCards Identifiers for GCSH Gene

  • GC16M072048
  • GC16M082076
  • GC16M080854
  • GC01M165211
  • GC16M080896
  • GC16M079673
  • GC16M081115
  • GC16M066872

Summaries for GCSH Gene

Entrez Gene Summary for GCSH 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 H protein, which transfers the methylamine group of glycine from the P protein to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH). Two transcript variants, one protein-coding and the other probably not protein-coding,have been found for this gene. Also, several transcribed and non-transcribed pseudogenes of this gene exist throughout the genome.[provided by RefSeq, Jan 2010]

GeneCards Summary for GCSH Gene

GCSH (Glycine Cleavage System Protein H) is a Protein Coding gene. Diseases associated with GCSH 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 enzyme binding and aminomethyltransferase activity. An important paralog of this gene is ENSG00000260643.

UniProtKB/Swiss-Prot for GCSH Gene

  • The glycine cleavage system catalyzes the degradation of glycine. The H protein (GCSH) shuttles the methylamine group of glycine from the P protein (GLDC) to the T protein (GCST).

Gene Wiki entry for GCSH Gene

Additional gene information for GCSH Gene

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

Genomics for GCSH Gene

Regulatory Elements for GCSH Gene

Enhancers for GCSH 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
GH16H081003 1.4 ENCODE dbSUPER 7 +90.3 90268 5.6 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D GLIS1 RCOR2 NBN ENSG00000260213 ATMIN CMC2 CENPN GCSH ENSG00000278985
GH16H081623 2 FANTOM5 Ensembl ENCODE dbSUPER 4.6 -529.1 -529053 4 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B ZNF766 ZNF143 FOS JUNB CMIP GCSH PLCG2 ENSG00000279841 ENSG00000279294
GH16H081094 1.1 ENCODE 7.3 +0.1 119 2.7 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF766 ZNF143 ZNF207 FOS ATMIN PKD1L2 GCSH ENSG00000260643
GH16H081691 1.3 Ensembl ENCODE dbSUPER 5 -598.8 -598823 7.6 HDGF CTCF MXI1 RB1 ARID4B SIN3A MAX RAD21 RELA FOSL1 CMIP GCSH GC16M081715 LOC100129617
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GCSH on UCSC Golden Path with GeneCards custom track

Promoters for GCSH Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000088408 425 1601 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF766 ZNF143 ZNF207 FOS

Genomic Locations for GCSH Gene

Genomic Locations for GCSH Gene
14,488 bases
Minus strand

Genomic View for GCSH Gene

Genes around GCSH on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for GCSH Gene

Proteins for GCSH Gene

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

    Protein Symbol:
    Recommended name:
    Glycine cleavage system H protein, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q9H1E9

    Protein attributes for GCSH Gene

    173 amino acids
    Molecular mass:
    18885 Da
    Name=(R)-lipoate; Xref=ChEBI:CHEBI:83088;
    Quaternary structure:
    • Interacts with GLDC (By similarity). The glycine cleavage system is composed of four proteins: P (GLDC), T (GCST), L (DLD) and H (GCSH).

neXtProt entry for GCSH Gene

Post-translational modifications for GCSH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GCSH Gene

Domains & Families for GCSH Gene

Gene Families for GCSH Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



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

Function for GCSH Gene

Molecular function for GCSH Gene

UniProtKB/Swiss-Prot Function:
The glycine cleavage system catalyzes the degradation of glycine. The H protein (GCSH) shuttles the methylamine group of glycine from the P protein (GLDC) to the T protein (GCST).

Phenotypes From GWAS Catalog for GCSH Gene

Gene Ontology (GO) - Molecular Function for GCSH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004047 aminomethyltransferase activity TAS 3348809
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with GCSH: view
genes like me logo Genes that share phenotypes with GCSH: view

Human Phenotype Ontology for GCSH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for GCSH Gene

miRTarBase miRNAs that target GCSH

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for GCSH Gene

Localization for GCSH Gene

Subcellular locations from UniProtKB/Swiss-Prot for GCSH 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 GCSH gene
Compartment Confidence
mitochondrion 5
extracellular 1

Gene Ontology (GO) - Cellular Components for GCSH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion TAS,IEA 3348809
GO:0005759 mitochondrial matrix TAS --
GO:0005960 glycine cleavage complex IEA --
genes like me logo Genes that share ontologies with GCSH: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GCSH Gene

Pathways & Interactions for GCSH Gene

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

Gene Ontology (GO) - Biological Process for GCSH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006546 glycine catabolic process TAS 1671321
GO:0009249 protein lipoylation IDA 1671321
GO:0019464 glycine decarboxylation via glycine cleavage system IEA --
GO:0032259 methylation IEA --
GO:0034641 cellular nitrogen compound metabolic process TAS --
genes like me logo Genes that share ontologies with GCSH: view

No data available for SIGNOR curated interactions for GCSH Gene

Drugs & Compounds for GCSH Gene

(9) Drugs for GCSH Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 243
Ammonia Approved Pharma 0
Carbon dioxide Approved, Vet_approved Pharma 0
Lipoic Acid Approved Nutra 0
Tetrahydrofolic acid Approved Nutra 0

(2) Additional Compounds for GCSH Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-Methylene-THF
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with GCSH: view

Transcripts for GCSH Gene

Unigene Clusters for GCSH Gene

Glycine cleavage system protein H (aminomethyl carrier):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for GCSH Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GCSH Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for GCSH Gene

This gene is overexpressed in Liver, secretome (23.9) and Brain (12.1).

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

NURSA nuclear receptor signaling pathways regulating expression of GCSH Gene:


SOURCE GeneReport for Unigene cluster for GCSH Gene:


Evidence on tissue expression from TISSUES for GCSH Gene

  • Liver(4.7)
  • Muscle(4.3)
  • Nervous system(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GCSH 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 GCSH: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for GCSH Gene

Orthologs for GCSH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GCSH Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GCSH 33 34
  • 99.04 (n)
(Bos Taurus)
Mammalia GCSH 34
  • 90 (a)
LOC101905887 33
  • 89.84 (n)
-- 34
  • 87 (a)
-- 34
  • 87 (a)
-- 34
  • 85 (a)
-- 34
  • 80 (a)
-- 34
  • 79 (a)
(Canis familiaris)
Mammalia GCSH 33 34
  • 89.6 (n)
(Ornithorhynchus anatinus)
Mammalia GCSH 34
  • 87 (a)
(Rattus norvegicus)
Mammalia Gcsh 33
  • 85.1 (n)
(Mus musculus)
Mammalia Gcsh 33 16 34
  • 83.73 (n)
(Gallus gallus)
Aves -- 34
  • 78 (a)
GCSH 33 34
  • 76.89 (n)
(Anolis carolinensis)
Reptilia GCSH 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia gcsh 33
  • 70.41 (n)
(Danio rerio)
Actinopterygii gcsha 33
  • 68.4 (n)
gcshb 34
  • 60 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006548 33
  • 55.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta ppl 35 33 34
  • 55.07 (n)
(Caenorhabditis elegans)
Secernentea F52A8.5 35 33 34
  • 55.88 (n)
gcsh-1 34
  • 41 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV3 33 34 36
  • 51.59 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A03597g 33
  • 49.46 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR396W 33
  • 46.61 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G35120 33
  • 54.89 (n)
(Oryza sativa)
Liliopsida Os02g0170100 33
  • 56.88 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv3 33
  • 55.1 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08877 33
  • 47.74 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 31 (a)
Species where no ortholog for GCSH was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GCSH Gene

Gene Tree for GCSH (if available)
Gene Tree for GCSH (if available)

Paralogs for GCSH Gene

Variants for GCSH Gene

Sequence variations from dbSNP and Humsavar for GCSH Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs769222264 Pathogenic 81,090,603(+) TACCT(A/G)TGCAA nc-transcript-variant, reference, stop-gained
rs886039730 Pathogenic 81,096,278(-) CGAAC(A/G)TGGCG nc-transcript-variant, reference, missense
rs386833859 Likely pathogenic 81,082,964(-) TTGCA(G/T)GTTGG reference, missense, splice-acceptor-variant
rs202181338 Benign 81,084,602(+) AGTGG(-/A)AAAAA intron-variant
rs1000023343 -- 81,096,242(+) GCAGA(C/G)CAGGG nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv978006 CNV duplication 23825009
nsv958835 CNV deletion 24416366
nsv1138468 CNV deletion 24896259
nsv1127517 CNV deletion 24896259
nsv1070359 CNV deletion 25765185
nsv1067144 CNV loss 25217958
nsv1062724 CNV gain 25217958
esv6143 CNV loss 19470904
esv3639309 CNV loss 21293372
esv3553747 CNV deletion 23714750
esv2751615 CNV gain 17911159
esv2714774 CNV deletion 23290073
esv2490578 CNV deletion 19546169
esv2422360 CNV duplication 17116639
esv2127465 CNV deletion 18987734
esv1126856 CNV deletion 17803354
esv1003113 CNV deletion 20482838

Variation tolerance for GCSH Gene

Residual Variation Intolerance Score: 49.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.00; 60.15% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GCSH 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 GCSH Gene

Disorders for GCSH Gene

MalaCards: The human disease database

(8) MalaCards diseases for GCSH Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
glycine encephalopathy
  • non-ketotic hyperglycinemia
  • d-glycerate kinase deficiency
neonatal glycine encephalopathy
  • classic glycine encephalopathy
infantile glycine encephalopathy
  • infantile nkh
glycine encephalopathy with normal serum glycine
  • atypical glycine encephalopathy
- elite association - COSMIC cancer census association via MalaCards
Search GCSH 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. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for GCSH

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 GCSH: view

No data available for Genatlas for GCSH Gene

Publications for GCSH Gene

  1. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S … Matsubara Y (Human mutation 2006) 3 22 45 60
  2. The glycine cleavage system: structure of a cDNA encoding human H-protein, and partial characterization of its gene in patients with hyperglycinemias. (PMID: 1671321) Koyata H … Hiraga K (American journal of human genetics 1991) 2 3 4 60
  3. The primary structure of human H-protein of the glycine cleavage system deduced by cDNA cloning. (PMID: 2025283) Fujiwara K … Motokawa Y (Biochemical and biophysical research communications 1991) 2 3 4 60
  4. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. (PMID: 19844255) Dastani Z … Genest J (European journal of human genetics : EJHG 2010) 3 45 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for GCSH Gene

Sources for GCSH Gene

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