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

Gene ID: 27232, updated on 7-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42960754..42963880)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42789900..42793018)
105.20220307 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
  • 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. Chemical Biopsy for GNMT as Noninvasive and Tumorigenesis-Relevant Diagnosis of Liver Cancer. Oh S, et al. Anal Chem, 2023 Jan 17. PMID 36602057
  2. Common polymorphism in the glycine N-methyltransferase gene as a novel risk factor for cleft lip with or without cleft palate. Karas KuĹľeliÄŤki N, et al. Int J Oral Maxillofac Surg, 2018 Nov. PMID 30318092
  3. Genetic polymorphisms of the glycine N-methyltransferase and prostate cancer risk in the health professionals follow-up study. Chen M, et al. PLoS One, 2014. PMID 24800880, Free PMC Article
  4. 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
  5. 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

See all (63) 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
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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_2023_10

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

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