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

    Gene ID: 27232, updated on 28-Oct-2024

    Summary

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    Official Symbol
    GNMTprovided by HGNC
    Official Full Name
    glycine N-methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:4415
    See related
    Ensembl:ENSG00000124713 MIM:606628; AllianceGenome:HGNC:4415
    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
    mouse all
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    Genomic context

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    See GNMT in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42960754..42963880)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42789900..42793018)
    RS_2024_09 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 long intergenic non-protein coding RNA 2976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42928211-42928712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24581 Neighboring gene RPL24 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42935679-42935875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42938260-42939130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:42939131-42939999 Neighboring gene peroxisomal biogenesis factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42946179-42947120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24582 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42947525-42947721 Neighboring gene uncharacterized LOC124900215 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42948960-42949178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17212 Neighboring gene Sharpr-MPRA regulatory region 14905 Neighboring gene protein phosphatase 2 regulatory subunit B'delta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42979352-42979852 Neighboring gene male-enhanced antigen 1

    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 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. Glycine N -methyltransferase deficiency: a new patient with a novel mutation. Augoustides-Savvopoulou P, et al. J Inherit Metab Dis, 2003. PMID 14739680
    2. Glycine-N methyltransferase expression in HepG2 cells is involved in methyl group homeostasis by regulating transmethylation kinetics and DNA methylation. Wang YC, et al. J Nutr, 2011 May. PMID 21411609
    3. A DNA methylation signature associated with the epigenetic repression of glycine N-methyltransferase in human hepatocellular carcinoma. Huidobro C, et al. J Mol Med (Berl), 2013 Aug. PMID 23475283
    4. Androgen response element of the glycine N-methyltransferase gene is located in the coding region of its first exon. Lee CM, et al. Biosci Rep, 2013 Sep 17. PMID 23883094, Free PMC Article
    5. Characterisation of the androgen regulation of glycine N-methyltransferase in prostate cancer cells. Ottaviani S, et al. J Mol Endocrinol, 2013 Dec. PMID 23997240, Free PMC Article

    See all (65) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ERVK13-1/miR-873-5p/GNMT Axis Promotes Metastatic Potential in Human Bladder Cancer though Sarcosine Production.
      Title: ERVK13-1/miR-873-5p/GNMT Axis Promotes Metastatic Potential in Human Bladder Cancer though Sarcosine Production.
    2. Folic Acid Ameliorates Renal Injury in Experimental Obstructive Nephropathy: Role of Glycine N-Methyltransferase.
      Title: Folic Acid Ameliorates Renal Injury in Experimental Obstructive Nephropathy: Role of Glycine N-Methyltransferase.
    3. Chemical Biopsy for GNMT as Noninvasive and Tumorigenesis-Relevant Diagnosis of Liver Cancer.
      Title: Chemical Biopsy for GNMT as Noninvasive and Tumorigenesis-Relevant Diagnosis of Liver Cancer.
    4. Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis.
      Title: Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis.
    5. Polymorphisms in GNMT and DNMT3b are associated with methotrexate treatment outcome in plaque psoriasis.
      Title: Polymorphisms in GNMT and DNMT3b are associated with methotrexate treatment outcome in plaque psoriasis.
    6. Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
      Title: Total liver phosphatidylcholine content associates with non-alcoholic steatohepatitis and glycine N-methyltransferase expression.
    7. miR-224 can target the glycine N-methyltransferase (GNMT) mRNA coding sequence and plays an important role in GNMT suppression during liver tumorigenesis
      Title: MicroRNA-224 down-regulates Glycine N-methyltransferase gene expression in Hepatocellular Carcinoma.
    8. Exosomal miR-224 can decrease the expression of GNMT by directly targeting the 3'-UTR of GNMT mRNA to promote the proliferation and invasion of hepatocellular carcinoma (HCC) cells. In addition, serum exosomal miR-224 may be used as a biomarker for the diagnosis of HCC and a prognostic factor for patients with HCC.
      Title: Mechanism of exosomal microRNA-224 in development of hepatocellular carcinoma and its diagnostic and prognostic value.
    9. Common glycine N-methyltransferase variant genotypes increase the risk of cleft lip with or without cleft palate.
      Title: Common polymorphism in the glycine N-methyltransferase gene as a novel risk factor for cleft lip with or without cleft palate.
    10. Elevated GNMT protein expression is associated with pathogenesis of hepatocellular carcinoma.
      Title: Characterization of the GNMT-HectH9-PREX2 tripartite relationship in the pathogenesis of hepatocellular carcinoma.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    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 N-methyltransferase deficiency
    MedGen: C1847720 OMIM: 606664 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.
    EBI GWAS Catalog

    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

    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

    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
    		  
    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
    		  
    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
    		  
    enables glycine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    involved_in S-adenosylmethionine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in S-adenosylmethionine metabolic process IDA
    Inferred from Direct Assay
    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
    		  
    involved_in protein homotetramerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein homotetramerization IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in protein modification process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of gluconeogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sarcosine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    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_001318865.2 → NP_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/TrEMBL
      A0A0S2Z5F2
      Conserved Domains (1) summary
      pfam12847
      Location:58 → 158
      Methyltransf_18; Methyltransferase domain

    2. NM_018960.6 → NP_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, Q5T8W2, Q9NNZ1, Q9NS24
      UniProtKB/TrEMBL
      V9HW60
      Related
      ENSP00000361894.3, ENST00000372808.4
      Conserved Domains (2) summary
      COG4976
      Location:16 → 95
      COG4976; Predicted methyltransferase, contains TPR repeat [General function prediction only]
      pfam13649
      Location:61 → 171
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      42789900..42793018
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14749.3 GenPept UniProtKB/Swiss-Prot:Q14749

    Gene LinkOut

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

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