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    AMT aminomethyltransferase [ Homo sapiens (human) ]

    Gene ID: 275, updated on 11-May-2013
    Official Symbol
    AMTprovided by HGNC
    Official Full Name
    aminomethyltransferaseprovided by HGNC
    Primary source
    HGNC:473
    See related
    Ensembl:ENSG00000145020; HPRD:01997; MIM:238310; Vega:OTTHUMG00000156847
    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; 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]
    Location :
    3p21.2-p21.1
    Sequence :
    Chromosome: 3; NC_000003.11 (49454211..49460111, complement)

    Chromosome 3 - NC_000003.11Genomic Context describing neighboring genes Neighboring gene ras homolog family member A Neighboring gene T-cell leukemia translocation altered Neighboring gene nicolin 1 Neighboring gene dystroglycan 1 (dystrophin-associated glycoprotein 1) Neighboring gene BSN antisense RNA 2 (head to head)

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Non-ketotic hyperglycinemia

    Summary from GeneReviews: Glycine Encephalopathy Go to GeneReviews

    Disease Characteristics
    Glycine encephalopathy, also known as nonketotic hyperglycinemia (NKH), is an inborn error of glycine metabolism in which large quantities of glycine accumulate in all body tissues, including the brain. The majority of glycine encephalopathy presents in the neonatal period (85% as the neonatal severe form and 15% as the neonatal mild form). Of those presenting in infancy, 50% have the infantile mild form and 50% have the infantile severe form. Overall, 20% of all children presenting as either neonates or infants have a less severe outcome, defined as developmental quotient greater than 20. A minority have atypical forms. The neonatal form manifests in the first hours to days of life with progressive lethargy, hypotonia, and myoclonic jerks leading to apnea and often death. Surviving infants have profound intellectual disability and intractable seizures. The infantile form is characterized by hypotonia, developmental delay, and seizures. The atypical forms range from milder disease, with onset from late infancy to adulthood, to rapidly progressing and severe disease with late onset.
    Diagnosis Testing
    Glycine encephalopathy is suspected in individuals with elevated glycine concentration in blood and CSF. An increase in CSF glycine concentration together with an increased CSF-to-plasma glycine ratio suggests the diagnosis. Enzymatic confirmation of the diagnosis relies on measurement of glycine cleavage (GCS) enzyme activity in liver obtained by open biopsy or autopsy. The vast majority of affected individuals have no detectable enzyme activity. The three genes known to be associated with glycine encephalopathy are: GLDC (encoding the P-protein component of the GCS complex and accounting for 70%-75% of disease), AMT (encoding the T-protein component of the GCS complex and accounting for ~20% of disease), and GCSH (encoding the H-protein component of the GCS complex and accounting for <1% of disease). Molecular genetic testing of all three genes is available on a clinical basis. About 5% of persons with-enzyme proven NKH do not have a mutation in any of these three genes.
    Genetic Counseling
    Glycine encephalopathy is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Once an at-risk sib is known to be unaffected, the chance of his/her being a carrier is 2/3. Most individuals with glycine encephalopathy do not reproduce. Carrier testing and prenatal testing are possible if the disease-causing mutations in the family are known.
    References

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    aminomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    transaminase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    glycine catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    aminomethyltransferase, mitochondrial
    Names
    aminomethyltransferase, mitochondrial
    glycine cleavage system T protein
    glycine cleavage system protein T
    NP_000472.2
    NP_001158182.1
    NP_001158183.1
    NP_001158184.1

    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)

    mRNA and Protein(s)

    1. NM_000481.3NP_000472.2  aminomethyltransferase, mitochondrial isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
      Source sequence(s)
      D13811, DC387800, GD148179
      Consensus CDS
      CCDS2797.1
      UniProtKB/Swiss-Prot
      P48728
      Related
      ENSP00000273588, OTTHUMP00000210791, ENST00000273588, OTTHUMT00000346216
      Conserved Domains (2) summary
      PLN02319
      Location:16400
      Blast Score: 1304
      PLN02319; aminomethyltransferase
      pfam08669
      Location:301392
      Blast Score: 263
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    2. NM_001164710.1NP_001158182.1  aminomethyltransferase, mitochondrial isoform 2 precursor

      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/Swiss-Prot
      P48728
      Related
      ENSP00000415619, OTTHUMP00000210793, ENST00000458307, OTTHUMT00000346219
      Conserved Domains (2) summary
      PLN02319
      Location:16356
      Blast Score: 1094
      PLN02319; aminomethyltransferase
      pfam08669
      Location:257348
      Blast Score: 261
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    3. NM_001164711.1NP_001158183.1  aminomethyltransferase, mitochondrial isoform 3 precursor

      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/Swiss-Prot
      P48728
      Related
      ENSP00000443200, ENST00000538581
      Conserved Domains (2) summary
      pfam01571
      Location:29235
      Blast Score: 523
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:245336
      Blast Score: 259
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    4. NM_001164712.1NP_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/Swiss-Prot
      P48728
      Related
      ENSP00000378747, ENST00000395338
      Conserved Domains (2) summary
      PLN02319
      Location:16379
      Blast Score: 1207
      PLN02319; aminomethyltransferase
      pfam08669
      Location:301379
      Blast Score: 236
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain

    RNA

    1. NR_028435.1 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, DC387800, GD148179

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000003.11 Reference GRCh37.p10 Primary Assembly

      Range
      49454211..49460111, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000135.1 Alternate HuRef

      Range
      49513933..49519839, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018914.1 Alternate CHM1_1.0

      Range
      49386664..49392412, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

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