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    GNMT glycine N-methyltransferase [ Homo sapiens (human) ]

    Gene ID: 27232, updated on 26-Jul-2021

    Summary

    Official Symbol
    GNMTprovided by HGNC
    Official Full Name
    glycine N-methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:4415
    See related
    Ensembl:ENSG00000124713 MIM:606628
    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
    HEL-S-182mP
    Summary
    The protein encoded by this gene is an enzyme that catalyzes the conversion of S-adenosyl-L-methionine (along with glycine) to S-adenosyl-L-homocysteine and sarcosine. This protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between the upstream CNPY3 (canopy FGF signaling regulator 3) gene and this gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
    Expression
    Biased expression in liver (RPKM 73.9), pancreas (RPKM 27.4) and 1 other tissue See more
    Orthologs
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    Genomic context

    See GNMT in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (42960754..42963880)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42928492..42931618)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CNPY3-GNMT readthrough Neighboring gene canopy FGF signaling regulator 3 Neighboring gene RPL24 pseudogene 4 Neighboring gene peroxisomal biogenesis factor 6 Neighboring gene male-enhanced antigen 1 Neighboring gene protein phosphatase 2 regulatory subunit B'delta Neighboring gene kelch domain containing 3

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.
    GeneReviews: Not available
    Glycine N-methyltransferase deficiency
    MedGen: C1847720 OMIM: 606664 GeneReviews: Not available
    Compare labs

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough CNPY3-GNMT

    Readthrough gene: CNPY3-GNMT, Included gene: CNPY3

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables folic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables glycine N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables glycine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables glycine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables glycine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in S-adenosylhomocysteine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in S-adenosylmethionine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in S-adenosylmethionine metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular protein modification process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in glycogen metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in methionine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in one-carbon metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein homotetramerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein homotetramerization IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    involved_in regulation of gluconeogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in sarcosine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    glycine N-methyltransferase
    Names
    epididymis secretory sperm binding protein Li 182mP
    NP_001305794.1
    NP_061833.1

    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_008396.1 RefSeqGene

      Range
      4993..8119
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318865.2NP_001305794.1  glycine N-methyltransferase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC032627, HY010451, KU178604
      UniProtKB/Swiss-Prot
      Q14749
      UniProtKB/TrEMBL
      A0A0S2Z5F2
      Conserved Domains (1) summary
      pfam12847
      Location:58158
      Methyltransf_18; Methyltransferase domain
    2. NM_018960.6NP_061833.1  glycine N-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_061833.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC032627, HY010451
      Consensus CDS
      CCDS4876.1
      UniProtKB/Swiss-Prot
      Q14749
      UniProtKB/TrEMBL
      V9HW60
      Related
      ENSP00000361894.3, ENST00000372808.4
      Conserved Domains (2) summary
      COG4976
      Location:1695
      COG4976; Predicted methyltransferase, contains TPR repeat [General function prediction only]
      pfam13649
      Location:61171
      Methyltransf_25; Methyltransferase domain

    RNA

    1. NR_134899.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC032627, HY010451, KU178605

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

      Range
      42960754..42963880
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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