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Aliases for AMT Gene

Aliases for AMT Gene

  • Aminomethyltransferase 2 3 5
  • Glycine Cleavage System T Protein 3 4
  • GCST 3 4
  • GCVT 3 4
  • Aminomethyltransferase (Glycine Cleavage System Protein T) 2
  • Aminomethyltransferase, Mitochondrial 3
  • Glycine Cleavage System Protein T 2
  • EC 4
  • GCE 3
  • NKH 3

External Ids for AMT Gene

Previous GeneCards Identifiers for AMT Gene

  • GC03P048869
  • GC03M049308
  • GC03M049413
  • GC03M049429

Summaries for AMT Gene

Entrez Gene Summary for AMT Gene

  • This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

GeneCards Summary for AMT Gene

AMT (Aminomethyltransferase) is a Protein Coding gene. Diseases associated with AMT 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 transaminase activity and aminomethyltransferase activity. An important paralog of this gene is DMGDH.

UniProtKB/Swiss-Prot for AMT Gene

  • The glycine cleavage system catalyzes the degradation of glycine.

Additional gene information for AMT Gene

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

Genomics for AMT Gene

GeneHancer (GH) Regulatory Elements for AMT Gene

Promoters and enhancers for AMT 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
GH03J049409 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 695.1 +8.9 8946 8.9 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 AMT TCTA RHOA CCDC71 WDR6 SEMA3F-AS1 QRICH1 INKA1 RBM5 DAG1
GH03J049420 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 695.5 +0.8 814 3.1 FOXA2 ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 ETS1 SLC30A9 ZNF143 AMT GC03P049421 WDR6 INKA1 RNA5SP130 DAG1 LAMB2 MST1 ENSG00000283189 NICN1
GH03J049421 Promoter/Enhancer 1.1 EPDnew dbSUPER 650.7 +3.7 3669 0.1 ESRRA SAP130 JUN DPF2 TEAD3 CTBP1 FOS NR2F6 RXRB AMT RNA5SP130 DAG1 LAMB2 GC03P049421 RHOA ENSG00000283189
GH03J049419 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.7 +2.9 2852 0.1 AMT GC03P049421 RNA5SP130 DAG1 LAMB2 ENSG00000283189 RHOA
GH03J049338 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 71.7 +76.7 76703 14.7 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A USP4 AMT QRICH1 RBM6 RBM5 IP6K2 ATRIP USP19 WDR6 BSN-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AMT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AMT gene promoter:
  • AP-1
  • GR-beta
  • GR-alpha
  • GR
  • STAT5A
  • PPAR-gamma2
  • PPAR-gamma1
  • c-Jun
  • ATF-2
  • SRF

Genomic Locations for AMT Gene

Genomic Locations for AMT Gene
5,979 bases
Minus strand
5,976 bases
Minus strand

Genomic View for AMT Gene

Genes around AMT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for AMT Gene

Proteins for AMT Gene

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

    Protein Symbol:
    Recommended name:
    Aminomethyltransferase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • A8K3I5
    • B4DE61
    • B4DJQ0
    • E9PBG1
    • Q96IG6

    Protein attributes for AMT Gene

    403 amino acids
    Molecular mass:
    43946 Da
    Quaternary structure:
    • The glycine cleavage system is composed of four proteins: P, T, L and H.

    Three dimensional structures from OCA and Proteopedia for AMT Gene

    Alternative splice isoforms for AMT Gene


neXtProt entry for AMT Gene

Post-translational modifications for AMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for AMT Gene

Domains & Families for AMT Gene

Gene Families for AMT Gene

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

Graphical View of Domain Structure for InterPro Entry



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

Function for AMT Gene

Molecular function for AMT Gene

UniProtKB/Swiss-Prot Function:
The glycine cleavage system catalyzes the degradation of glycine.
UniProtKB/Swiss-Prot CatalyticActivity:
[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH(3).
GENATLAS Biochemistry:
amino-methyltransferase,tetrahydrofolate (THF) dependent,34kDa,T-protein,catalyzing the third step of the glycine cleavage system

Enzyme Numbers (IUBMB) for AMT Gene

Phenotypes From GWAS Catalog for AMT Gene

Gene Ontology (GO) - Molecular Function for AMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004047 aminomethyltransferase activity TAS --
GO:0008168 methyltransferase activity IEA --
GO:0008483 transaminase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with AMT: view
genes like me logo Genes that share phenotypes with AMT: view

Human Phenotype Ontology for AMT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for AMT

miRNA for AMT Gene

miRTarBase miRNAs that target AMT

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for AMT Gene

Localization for AMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for AMT 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 AMT gene
Compartment Confidence
mitochondrion 5
nucleus 4
peroxisome 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for AMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IDA,TAS --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with AMT: view

Pathways & Interactions for AMT Gene

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

Gene Ontology (GO) - Biological Process for AMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006546 glycine catabolic process TAS 9600239
GO:0019464 glycine decarboxylation via glycine cleavage system IMP 16051266
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with AMT: view

No data available for SIGNOR curated interactions for AMT Gene

Drugs & Compounds for AMT Gene

(23) Drugs for AMT Gene - From: DrugBank, ClinicalTrials, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra Target 0
Amikacin Approved, Investigational, Vet_approved Pharma 70
Betamethasone Approved, Vet_approved Pharma Glucocorticoid receptor agonist 213
Cefazolin Approved Pharma 126
Ammonia Approved Pharma 0

(3) Additional Compounds for AMT Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5,10-Methenyltetrahydrofolic acid
  • 5,10-Methenyl-THF
  • 5,10-Methenyltetrahydrofolate
  • anhydro-Leucovorin
  • anhydro-Leucovorin a
  • Anhydroleucovorin
  • (6R)-5,10-Methylenetetrahydrofolate
  • (6R)-5,10-Methylenetetrahydrofolic acid
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-hydrofolate
  • 5,10-Methylene-6-hydrofolic acid
Hydrogen Ion
  • H+
  • H(+)
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with AMT: view

Transcripts for AMT Gene

mRNA/cDNA for AMT Gene

Unigene Clusters for AMT Gene

Representative Sequences:

Clone Products

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

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11 ^ 12
SP1: - - - - -
SP2: - - - - -
SP3: - - - - - -
SP4: - - - - - - - -
SP5: - - - - - - -
SP6: - - - -
SP7: - - - - -
SP10: -

Relevant External Links for AMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for AMT Gene

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

Protein differential expression in normal tissues from HIPED for AMT Gene

This gene is overexpressed in NK cells (12.4), Heart (11.0), and Kidney (9.3).

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

Protein tissue co-expression partners for AMT Gene

NURSA nuclear receptor signaling pathways regulating expression of AMT Gene:


SOURCE GeneReport for Unigene cluster for AMT Gene:


Evidence on tissue expression from TISSUES for AMT Gene

  • Nervous system(4.7)
  • Intestine(4.3)
  • Heart(4.2)

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

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for AMT Gene

Orthologs for AMT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for AMT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia AMT 34 33
  • 99.67 (n)
(Canis familiaris)
Mammalia AMT 34 33
  • 88.59 (n)
(Bos Taurus)
Mammalia AMT 34 33
  • 87.74 (n)
(Rattus norvegicus)
Mammalia Amt 33
  • 84.78 (n)
(Mus musculus)
Mammalia Amt 16 34 33
  • 84.28 (n)
(Ornithorhynchus anatinus)
Mammalia AMT 34
  • 79 (a)
(Monodelphis domestica)
Mammalia AMT 34
  • 74 (a)
(Gallus gallus)
Aves AMT 34 33
  • 69.21 (n)
(Anolis carolinensis)
Reptilia AMT 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia amt 33
  • 66.85 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13933 33
(Danio rerio)
Actinopterygii amt 34 33
  • 66.21 (n)
wufc31f04 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6341 33
fruit fly
(Drosophila melanogaster)
Insecta CG6415 34 35 33
  • 55.61 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001124 33
  • 55.58 (n)
(Caenorhabditis elegans)
Secernentea CELE_F25B4.1 33
  • 53.24 (n)
F25B4.1 35
  • 53 (a)
gcst-1 34
  • 52 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV1 36 34 33
  • 48.09 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B06754g 33
  • 47.98 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G11860 33
  • 53.84 (n)
(Oryza sativa)
Liliopsida Os04g0623800 33
  • 57.53 (n)
Os.20702 33
(Zea mays)
Liliopsida Zm.4867 33
(Triticum aestivum)
Liliopsida Ta.20834 33
bread mold
(Neurospora crassa)
Ascomycetes NCU02727 33
  • 53.6 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv1 33
  • 48.64 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
Species where no ortholog for AMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for AMT Gene

Gene Tree for AMT (if available)
Gene Tree for AMT (if available)
Evolutionary constrained regions (ECRs) for AMT: view image

Paralogs for AMT Gene

Paralogs for AMT Gene Pseudogenes for AMT Gene

genes like me logo Genes that share paralogs with AMT: view

Variants for AMT Gene

Sequence variations from dbSNP and Humsavar for AMT Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1056820947 hyperglycinemia (NKH) [MIM:605899] 49,417,965(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs10640 benign, Non-ketotic hyperglycinemia 49,416,844(-) G/A/C/T 3_prime_UTR_variant, non_coding_transcript_variant
rs1126422 Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,421,551(-) G/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs114057053 uncertain-significance, Non-ketotic hyperglycinemia 49,416,995(-) G/A 3_prime_UTR_variant, non_coding_transcript_variant
rs116192290 benign, Non-ketotic hyperglycinemia, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,419,325(-) C/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv834687 CNV loss 17160897
esv3407171 CNV insertion 20981092
esv3310568 CNV novel sequence insertion 20981092

Variation tolerance for AMT Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.36; 41.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AMT 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 AMT Gene

Disorders for AMT Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
glycine encephalopathy
  • gce
glycine encephalopathy with normal serum glycine
  • atypical glycine encephalopathy
neonatal glycine encephalopathy
  • classic glycine encephalopathy
infantile glycine encephalopathy
  • infantile nkh
early myoclonic encephalopathy
  • epileptic seizures - myoclonic
- elite association - COSMIC cancer census association via MalaCards
Search AMT 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:10873393, ECO:0000269 PubMed:11286506, ECO:0000269 PubMed:16051266, ECO:0000269 PubMed:26371980, ECO:0000269 PubMed:28244183, ECO:0000269 PubMed:8005589, ECO:0000269 PubMed:9600239, ECO:0000269 PubMed:9621520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for AMT

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 AMT: view

No data available for Genatlas for AMT Gene

Publications for AMT Gene

  1. Structure and chromosomal localization of the aminomethyltransferase gene (AMT) (PMID: 8188235) Nanao K … Hayasaka K (Genomics 1994) 2 3 4 22 58
  2. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S … Matsubara Y (Human mutation 2006) 3 22 44 58
  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 JR … James ER (Molecular genetics and metabolism 2001) 3 4 22 58
  4. Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population. (PMID: 19367581) So HC … Sham PC (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2010) 3 44 58
  5. Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PMID: 20307617) Morgan AR … Ferguson LR (Human immunology 2010) 3 44 58

Products for AMT Gene

Sources for AMT Gene

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