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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
not available
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

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