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AMT Gene(Protein Coding)

Aminomethyltransferase

GCID:
GC03M049454
GIFtS:
62
Genes Participants
UDN Logo

Aliases for AMT Gene

Aliases for AMT Gene

  • Aminomethyltransferase 2 3 5
  • Glycine Cleavage System T Protein 3 4
  • EC 2.1.2.10 4 61
  • GCST 3 4
  • GCVT 3 4
  • Aminomethyltransferase (Glycine Cleavage System Protein T) 2
  • Aminomethyltransferase, Mitochondrial 3
  • Glycine Cleavage System Protein T 2
  • 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 Infantile Glycine Encephalopathy. Among its related pathways are Glyoxylate metabolism and glycine degradation and One carbon pool by folate. 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.

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

Products:

  1. Regulatory Element

Regulatory Elements for AMT Gene

Enhancers for AMT 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
GH03G049338 1.9 FANTOM5 ENCODE dbSUPER 53.5 +76.7 76704 14.7 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC AMT QRICH1 IMPDH2 DALRD3 RHOA WDR6 NICN1 USP4 ENSG00000230454 RHOA-IT1
GH03G049409 1.6 Ensembl ENCODE dbSUPER 45.2 +8.9 8947 8.9 HDGF PKNOX1 FOXA2 ARNT CREB3L1 SIN3A ARID4B DMAP1 YY1 SLC30A9 AMT CCDC71 WDR6 SEMA3F-AS1 QRICH1 FAM212A DAG1 RNA5SP130 TMEM115 USP4
GH03G049467 1.3 ENCODE dbSUPER 55.6 -47.2 -47172 5.2 HDGF PKNOX1 FOXA2 ARNT CREB3L1 ARID4B SIN3A YY1 ZNF143 ZNF207 AMT WDR6 LAMB2 MST1 USP4 DAG1 PIR41851
GH03G049237 1.7 FANTOM5 Ensembl ENCODE 40.6 +183.6 183553 2.9 PKNOX1 FOXA2 ARNT DMAP1 ZNF766 CBX5 NFYC REST ZNF592 KAT8 WDR6 AMT USP4 APEH DALRD3 ENSG00000235236 RHOA ARIH2 AMIGO3 ENSG00000270538
GH03G049458 1.5 Ensembl ENCODE dbSUPER 45 -38.6 -38618 5.6 HDGF FOXA2 PKNOX1 ATF1 MLX FEZF1 ZNF48 YY1 ETS1 ZNF121 AMT WDR6 FAM212A MST1 GC03M049467 RNA5SP130 NICN1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around AMT on UCSC Golden Path with GeneCards custom track

Promoters for AMT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152222 453 201 FOXA2 ATF1 ZFP64 ARID4B DMAP1 DNMT3B THRB YY1 SLC30A9 ZNF143

Transcription factor binding sites by QIAGEN in the AMT gene promoter:

Genomic Location for AMT Gene

Chromosome:
3
Start:
49,416,775 bp from pter
End:
49,422,753 bp from pter
Size:
5,979 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for AMT Gene

Proteins for AMT Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P48728-GCST_HUMAN
    Recommended name:
    Aminomethyltransferase, mitochondrial
    Protein Accession:
    P48728
    Secondary Accessions:
    • A8K3I5
    • B4DE61
    • B4DJQ0
    • E9PBG1
    • Q96IG6

    Protein attributes for AMT Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for AMT Gene

Protein Expression for AMT Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for AMT Gene

P48728:
  • KMPFVPT
  • ARDSLRLEAG
  • FAGWSLPVQY
  • LLALQGP
  • GYTGEDG
  • WTLGKRRR
  • PVEGSLSW
  • LYVVSNAGC

Post-translational modifications for AMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for AMT Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for AMT Gene

Protein Domains for AMT Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for AMT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P48728

UniProtKB/Swiss-Prot:

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

No data available for Gene Families for AMT Gene

Function for AMT Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for AMT Gene

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

Enzyme Numbers (IUBMB) 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

Phenotypes for AMT Gene

MGI mutant phenotypes for AMT:
inferred from 1 alleles
GenomeRNAi human phenotypes for AMT:
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

Flow Cytometry 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

Mitochondrion.

Subcellular locations from

COMPARTMENTS
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

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 --
GO:0046487 glyoxylate metabolic process TAS --
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

Products:

  1. Drug

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Tetrahydrofolic acid Approved Nutra Target, cofactor 0
Amikacin Approved, Vet_approved Pharma 66
Betamethasone Approved, Vet_approved Pharma Glucocorticoid receptor agonist 195
Cefazolin Approved Pharma 112
Carbon dioxide Approved, Vet_approved Pharma 0

(4) 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
 7444-29-3
5,10-Methylene-THF
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-Methylene-THF
 31690-11-6
Ammonia
  • Ammonia anhydrous
  • Ammonia inhalant
  • Ammonia solution strong [usan]
  • Ammonia water
  • Ammoniak
 7664-41-7
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with AMT: view

Transcripts for AMT Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for AMT Gene

(4) REFSEQ mRNAs :
(13) Additional mRNA sequences :
(246) Selected AceView cDNA sequences:
(57) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for AMT Gene

Aminomethyltransferase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry 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: - - - - -
SP8:
SP9:
SP10: -
SP11:

Relevant External Links for AMT Gene

GeneLoc Exon Structure for
AMT
ECgene alternative splicing isoforms for
AMT

Expression for AMT Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for AMT Gene
mRNA expression by BioGPS for AMT GenemRNA expression by GTEx 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, PaxDb, MaxQB, and MOPED for AMT Gene



Protein tissue co-expression partners for AMT Gene

NURSA nuclear receptor signaling pathways regulating expression of AMT Gene:

AMT

SOURCE GeneReport for Unigene cluster for AMT Gene:

Hs.102

Evidence on tissue expression from TISSUES for AMT Gene

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

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • epiglottis
  • head
  • neck
Thorax:
  • diaphragm
  • lung
General:
  • spinal cord
genes like me logo Genes that share expression patterns with AMT: view

Primer Products

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
chimpanzee
(Pan troglodytes)
 Mammalia AMT 34 35
  • 99.67 (n)
dog
(Canis familiaris)
 Mammalia AMT 34 35
  • 88.59 (n)
cow
(Bos Taurus)
 Mammalia AMT 34 35
  • 87.74 (n)
rat
(Rattus norvegicus)
 Mammalia Amt 34
  • 84.78 (n)
mouse
(Mus musculus)
 Mammalia Amt 34 16 35
  • 84.28 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia AMT 35
  • 79 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia AMT 35
  • 74 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves AMT 34 35
  • 69.21 (n)
lizard
(Anolis carolinensis)
 Reptilia AMT 35
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia amt 34
  • 66.85 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.13933 34
zebrafish
(Danio rerio)
 Actinopterygii amt 34 35
  • 66.21 (n)
wufc31f04 34
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.6341 34
fruit fly
(Drosophila melanogaster)
 Insecta CG6415 36 34 35
  • 55.61 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP001124 34
  • 55.58 (n)
worm
(Caenorhabditis elegans)
 Secernentea CELE_F25B4.1 34
  • 53.24 (n)
F25B4.1 36
  • 53 (a)
gcst-1 35
  • 52 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes GCV1 34 35 37
  • 48.09 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0B06754g 34
  • 47.98 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT1G11860 34
  • 53.84 (n)
rice
(Oryza sativa)
 Liliopsida Os04g0623800 34
  • 57.53 (n)
Os.20702 34
wheat
(Triticum aestivum)
 Liliopsida Ta.20834 34
corn
(Zea mays)
 Liliopsida Zm.4867 34
bread mold
(Neurospora crassa)
 Ascomycetes NCU02727 34
  • 53.6 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes gcv1 34
  • 48.64 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 47 (a)
 OneToOne
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

ENSEMBL:
Gene Tree for AMT (if available)
TreeFam:
Gene Tree for AMT (if available)

Paralogs for AMT Gene

Paralogs for AMT Gene

Pseudogenes.org 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 Sequence Context AA Info Type
rs116192290 Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,419,325(+) CACCT(C/T)CATCA nc-transcript-variant, reference, missense
rs121964981 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,419,042(-) GGCAG(A/G)CCTCT nc-transcript-variant, reference, missense
rs121964982 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,422,223(-) ACGGC(A/G/T)GGAAA intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs121964983 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,422,237(-) CTTCC(A/G)CCTGG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs121964984 Pathogenic, Non-ketotic hyperglycinemia (NKH) [MIM:605899] 49,419,022(-) GGAAT(C/G)ACATT nc-transcript-variant, reference, missense

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)

Relevant External Links for AMT Gene

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

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

Disorders for AMT Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
glycine encephalopathy
  • non-ketotic hyperglycinemia
infantile glycine encephalopathy
  • infantile nkh
neonatal glycine encephalopathy
  • classic glycine encephalopathy
atypical glycine encephalopathy
  • atypical nka
amt-related glycine encephalopathy
- elite association - COSMIC cancer census association via MalaCards
Search AMT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GCST_HUMAN
  • 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:8005589, ECO:0000269 PubMed:9600239, ECO:0000269 PubMed:9621520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for AMT

Genetic Association Database (GAD)
AMT
Human Genome Epidemiology (HuGE) Navigator
AMT
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
AMT
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 64
  2. Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia. (PMID: 16450403) Kure S. … Matsubara Y. (Hum. Mutat. 2006) 3 22 46 64
  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 J.R. … James E.R. (Mol. Genet. Metab. 2001) 3 4 22 64
  4. Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population. (PMID: 19367581) So H.C. … Sham P.C. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2010) 3 46 64
  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 S.D. … Anand S. (Diabetes Care 2010) 3 46 64

Products for AMT Gene

Sources for AMT Gene

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