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    AMT aminomethyltransferase [ Homo sapiens (human) ]

    Gene ID: 275, updated on 5-Mar-2024

    Summary

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    Official Symbol
    AMTprovided by HGNC
    Official Full Name
    aminomethyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:473
    See related
    Ensembl:ENSG00000145020 MIM:238310; AllianceGenome:HGNC:473
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GCE; NKH; GCE2; GCST; GCVT
    Summary
    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]
    Expression
    Ubiquitous expression in kidney (RPKM 16.6), liver (RPKM 14.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3p21.31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49416778..49422473, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49446157..49451857, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49454211..49459906, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr3:49395462-49396070 and GRCh37_chr3:49396071-49396679 Neighboring gene ras homolog family member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49423846-49424400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49424401-49424954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49426165-49426934 Neighboring gene Sharpr-MPRA regulatory region 7935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49455091-49455809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49458781-49459533 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49459534-49460287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19869 Neighboring gene T cell leukemia translocation altered Neighboring gene nicolin 1, tubulin polyglutamylase complex subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49496363-49497118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49498631-49499386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49502186-49502686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14366 Neighboring gene RNA, 5S ribosomal pseudogene 130 Neighboring gene dystroglycan 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49572171-49573169

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Structure and chromosomal localization of the aminomethyltransferase gene (AMT). Nanao K, et al. Genomics, 1994 Jan 1. PMID 8188235
    2. Isolation and sequence determination of cDNA encoding human T-protein of the glycine cleavage system. Hayasaka K, et al. Biochem Biophys Res Commun, 1993 Apr 30. PMID 7916605
    3. The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT. Coughlin CR 2nd, et al. Genet Med, 2017 Jan. PMID 27362913
    4. Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. Okamura-Ikeda K, et al. J Mol Biol, 2005 Sep 2. PMID 16051266
    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). Toone JR, et al. Mol Genet Metab, 2001 Apr. PMID 11286506

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The position and frequency of the breakpoint for CNVs correlated with intron size and presence of Alu elements. Missense mutations, most often recurring, were the most common type of disease-causing mutation in AMT
      Title: The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT.
    2. Data indicate no mutation was found in glycine cleavage system protein-H (GCSH) and suggest that mutations in both glycine decarboxylase (GLDC) and aminomethyltransferase (AMT) are the main cause of glycine encephalopathy in Malaysian population.
      Title: Mutation analysis of glycine decarboxylase, aminomethyltransferase and glycine cleavage system protein-H genes in 13 unrelated families with glycine encephalopathy.
    3. Two unique non-synonymous changes were identified in the AMT gene in patients with neural tube defects.
      Title: Mutations in genes encoding the glycine cleavage system predispose to neural tube defects in mice and humans.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China.
    6. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    8. Observational study of genotype prevalence. (HuGE Navigator)
      Title: Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia.
    9. x-ray crystallographic structure of human T-protein of glycine cleavage system
      Title: Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Glycine encephalopathy 2
    MedGen: C5830559 OMIM: 620398 GeneReviews: Not available
    		Compare labs
    Non-ketotic hyperglycinemia
    MedGen: C0751748 GeneReviews: Nonketotic Hyperglycinemia
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of aminomethyltransferase (AMT) by siRNA enhances HIV-1 replication in CD4+/CCR5+/CXCR4+ TZM-bl HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables aminomethyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables aminomethyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables transaminase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in glycine catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in glycine decarboxylation via glycine cleavage system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    aminomethyltransferase, mitochondrial
    Names
    glycine cleavage system T protein
    nonketotic hyperglycinemia
    NP_000472.2
    NP_001158182.1
    NP_001158183.1
    NP_001158184.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_015986.1 RefSeqGene

      Range
      5001..10901
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_537

    mRNA and Protein(s)

    1. NM_000481.4 → NP_000472.2  aminomethyltransferase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_000472.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
      Source sequence(s)
      D13811, GD148179
      Consensus CDS
      CCDS2797.1
      UniProtKB/Swiss-Prot
      A8K3I5, B4DE61, B4DJQ0, E9PBG1, P48728, Q96IG6
      UniProtKB/TrEMBL
      A0A1B0GTM2
      Related
      ENSP00000273588.3, ENST00000273588.9
      Conserved Domains (3) summary
      PLN02319
      Location:16 → 400
      PLN02319; aminomethyltransferase
      pfam01571
      Location:39 → 291
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:301 → 392
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

    2. NM_001164710.2 → NP_001158182.1  aminomethyltransferase, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_001158182.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AK296177, DC387800, GD148179
      Consensus CDS
      CCDS54584.1
      UniProtKB/TrEMBL
      B3KRJ7
      Related
      ENSP00000415619.2, ENST00000458307.6
      Conserved Domains (3) summary
      PLN02319
      Location:16 → 356
      PLN02319; aminomethyltransferase
      pfam01571
      Location:39 → 247
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:257 → 348
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

    3. NM_001164711.2 → NP_001158183.1  aminomethyltransferase, mitochondrial isoform 3 precursor

      See identical proteins and their annotated locations for NP_001158183.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
      Source sequence(s)
      AC104452, AK293481, DC387800, GD148179
      Consensus CDS
      CCDS54583.1
      UniProtKB/TrEMBL
      B4DGG9
      Related
      ENSP00000489758.1, ENST00000636522.1
      Conserved Domains (2) summary
      pfam01571
      Location:29 → 235
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:245 → 336
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

    4. NM_001164712.2 → NP_001158184.1  aminomethyltransferase, mitochondrial isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region that results in a frameshift compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      BC007546, DC387800
      Consensus CDS
      CCDS54585.1
      UniProtKB/TrEMBL
      A0A1B0GTA8
      Related
      ENSP00000378747.2, ENST00000395338.7
      Conserved Domains (3) summary
      PLN02319
      Location:16 → 379
      PLN02319; aminomethyltransferase
      pfam01571
      Location:39 → 291
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:301 → 379
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

    RNA

    1. NR_028435.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' coding region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK096062, GD148179
      Related
      ENST00000538581.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      49416778..49422473 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      49446157..49451857 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P48728.1 GenPept UniProtKB/Swiss-Prot:P48728

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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