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] See more...

Aliases for AMT Gene

Aliases for AMT Gene

  • Aminomethyltransferase 2 3 5
  • GCST 2 3 4
  • Aminomethyltransferase, Mitochondrial 3 4
  • Glycine Cleavage System T Protein 3 4
  • Nonketotic Hyperglycinemia 2 3
  • EC 4 51
  • GCVT 3 4
  • NKH 2 3
  • Aminomethyltransferase (Glycine Cleavage System Protein T) 2
  • Glycine Cleavage System Protein T 2
  • GCE 3
  • AMT 5

External Ids for AMT Gene

Previous GeneCards Identifiers for AMT Gene

  • GC03P048869
  • GC03M049308
  • GC03M049413
  • GC03M049429
  • GC03M049454

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 Atypical Glycine Encephalopathy. Among its related pathways are One carbon pool by folate and Glyoxylate and dicarboxylate metabolism. 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 Summary for AMT Gene

  • The glycine cleavage system catalyzes the degradation of glycine.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for AMT Gene

Genomics for AMT Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH03J049408 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 645.2 +9.4 9353 9.9 SP1 GATAD2A CTCF PRDM10 NFKBIZ KDM1A ZNF692 POLR2A BACH1 TARDBP AMT TCTA RHOA lnc-RHOA-1 WDR6 INKA1 RNA5SP130 DAG1 USP4 KLHDC8B
GH03J049420 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 645.4 +0.7 746 3.1 GATAD2A TFE3 ZNF143 RBFOX2 RXRB SP1 POLR2A GABPA FOXK2 SCRT2 AMT lnc-NICN1-2-001 lnc-NICN1-2-002 lnc-TCTA-1 WDR6 INKA1 RNA5SP130 DAG1 LAMB2 MST1
GH03J049421 Promoter/Enhancer 0.9 EPDnew dbSUPER 600.7 +3.6 3601 0.1 JUND CTBP1 JUN ESRRA SAP130 DPF2 NR2F1 RARA FOS ESR1 AMT RNA5SP130 DAG1 LAMB2 lnc-NICN1-2-001 RHOA lnc-RHOA-1 ENSG00000283189
GH03J049419 Promoter/Enhancer 0.5 EPDnew dbSUPER 600.7 +2.8 2784 0.1 AMT lnc-NICN1-2-001 RNA5SP130 DAG1 LAMB2 ENSG00000283189 RHOA lnc-RHOA-1
GH03J049338 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 63.2 +76.9 76884 16 RNF2 SP1 HNRNPL GATAD2A CTCF PRDM10 TFE3 LEF1 IKZF1 POLR2A USP4 lnc-TCTA-3 AMT WDR6 QRICH1 RBM6 ENSG00000235236 DALRD3 RHOA NICN1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around AMT on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for AMT

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

Genomic Locations for AMT Gene

Genomic Locations for AMT Gene
5,908 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

Selected DME Specific Peptides for AMT Gene


Post-translational modifications for AMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

Protein Domains for AMT Gene

  • Glycine cleavage T protein (aminomethyl transferase)

Suggested Antigen Peptide Sequences for AMT Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ34419 fis, clone HEART2008257, highly similar to Aminomethyltransferase, mitochondrial (EC (B3KRJ7_HUMAN)
  • Aminomethyltransferase (B4DE61_HUMAN)
  • Aminomethyltransferase (B4DGG9_HUMAN)
  • cDNA FLJ55081, highly similar to Aminomethyltransferase, mitochondrial (EC (B4DJQ0_HUMAN)
  • Aminomethyltransferase (E9PBG1_HUMAN)

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:
Reaction=(6S)-5,6,7,8-tetrahydrofolate + (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-[protein] = (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + (R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NH4(+); Xref=Rhea:RHEA:16945, Rhea:RHEA-COMP:10475, Rhea:RHEA-COMP:10492, ChEBI:CHEBI:15636, ChEBI:CHEBI:28938, ChEBI:CHEBI:57453, ChEBI:CHEBI:83100, ChEBI:CHEBI:83143; EC=; Evidence={ECO:0000269|PubMed:16051266};.
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:0005515 protein binding IEA --
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

CRISPR Products

miRNA for AMT Gene

miRTarBase miRNAs that target AMT

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for 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
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
golgi apparatus 1

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 TAS,IDA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved, Vet_approved Nutra Agonist, Full agonist, Enzyme, substrate 196
NADH Approved Nutra Target 0
Amikacin Approved, Investigational, Vet_approved Pharma 91
Betamethasone Approved, Vet_approved Pharma Glucocorticoid receptor agonist 275
Cefazolin Approved Pharma 163

(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

14 NCBI additional mRNA sequence :
57 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AMT

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

Expression for AMT Gene

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for AMT

SOURCE GeneReport for Unigene cluster for AMT Gene:


Evidence on tissue expression from TISSUES for AMT Gene

  • Nervous system(4.7)
  • Intestine(4.5)
  • Heart(4.4)
  • Skin(2.6)
  • Muscle(2.3)
  • Liver(2.1)
  • Kidney(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 30 31
  • 99.67 (n)
(Canis familiaris)
Mammalia AMT 30 31
  • 88.59 (n)
(Bos Taurus)
Mammalia AMT 30 31
  • 87.74 (n)
(Rattus norvegicus)
Mammalia Amt 30
  • 84.78 (n)
(Mus musculus)
Mammalia Amt 30 17 31
  • 84.28 (n)
(Ornithorhynchus anatinus)
Mammalia AMT 31
  • 79 (a)
(Monodelphis domestica)
Mammalia AMT 31
  • 74 (a)
(Gallus gallus)
Aves AMT 30 31
  • 69.21 (n)
(Anolis carolinensis)
Reptilia AMT 31
  • 68 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia amt 30
  • 66.85 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13933 30
(Danio rerio)
Actinopterygii amt 30 31
  • 66.21 (n)
wufc31f04 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6341 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG6415 30 31 32
  • 55.61 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001124 30
  • 55.58 (n)
(Caenorhabditis elegans)
Secernentea CELE_F25B4.1 30
  • 53.24 (n)
F25B4.1 32
  • 53 (a)
gcst-1 31
  • 52 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCV1 30 31 33
  • 48.09 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B06754g 30
  • 47.98 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT1G11860 30
  • 53.84 (n)
(Oryza sativa)
Liliopsida Os04g0623800 30
  • 57.53 (n)
Os.20702 30
(Triticum aestivum)
Liliopsida Ta.20834 30
(Zea mays)
Liliopsida Zm.4867 30
Bread mold
(Neurospora crassa)
Ascomycetes NCU02727 30
  • 53.6 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gcv1 30
  • 48.64 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 47 (a)
Species where no ortholog for AMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for AMT Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
623331 Pathogenic: Non-ketotic hyperglycinemia 49,422,429(-) CCA/C FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR_VARIANT
635296 Uncertain Significance: Non-ketotic hyperglycinemia 49,420,341(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
638882 Uncertain Significance: Non-ketotic hyperglycinemia 49,421,489(-) C/A INTRON_VARIANT
644213 Uncertain Significance: Non-ketotic hyperglycinemia 49,420,311(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
645153 Conflicting Interpretations: Non-ketotic hyperglycinemia 49,422,214(-) C/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for AMT Gene

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

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

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

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

Disorder Aliases PubMed IDs
glycine encephalopathy
  • gce
atypical glycine encephalopathy
  • atypical nka
cutis laxa, autosomal dominant 1
  • adcl1
early myoclonic encephalopathy
  • epileptic seizures - myoclonic
  • pntsu
- 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
Open Targets Platform
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 23
  2. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S … Matsubara Y (Human mutation 2006) 3 23 41
  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 23
  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 41
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41

Products for AMT Gene

Sources for AMT Gene