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Aliases for GNMT Gene

Aliases for GNMT Gene

  • Glycine N-Methyltransferase 2 3
  • EC 4 64
  • Epididymis Secretory Sperm Binding Protein Li 182mP 3
  • HEL-S-182mP 3

External Ids for GNMT Gene

Summaries for GNMT Gene

Entrez Gene Summary for GNMT Gene

  • 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. The encoded protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). [provided by RefSeq, Oct 2008]

GeneCards Summary for GNMT Gene

GNMT (Glycine N-Methyltransferase) is a Protein Coding gene. Diseases associated with GNMT include glycine n-methyltransferase deficiency and hypermethioninemia due to glycine n-methyltransferase deficiency. Among its related pathways are Glycine, serine and threonine metabolism. GO annotations related to this gene include folic acid binding and glycine N-methyltransferase activity.

UniProtKB/Swiss-Prot for GNMT Gene

  • Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.

Gene Wiki entry for GNMT Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GNMT Gene

Genomics for GNMT Gene

Genomic Location for GNMT Gene

42,960,758 bp from pter
42,963,880 bp from pter
3,123 bases
Plus strand

Genomic View for GNMT Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for GNMT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GNMT Gene

Regulatory Elements for GNMT Gene

Proteins for GNMT Gene

  • Protein details for GNMT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Glycine N-methyltransferase
    Protein Accession:
    Secondary Accessions:
    • Q5T8W2
    • Q9NNZ1
    • Q9NS24

    Protein attributes for GNMT Gene

    295 amino acids
    Molecular mass:
    32742 Da
    Quaternary structure:
    • Homotetramer.

    Three dimensional structures from OCA and Proteopedia for GNMT Gene

neXtProt entry for GNMT Gene

Proteomics data for GNMT Gene at MOPED

Post-translational modifications for GNMT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for GNMT Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains for GNMT Gene

Protein Domains for GNMT Gene


  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Glycine N-methyltransferase family.:
    • Q14749
genes like me logo Genes that share domains with GNMT: view

No data available for Gene Families for GNMT Gene

Function for GNMT Gene

Molecular function for GNMT Gene

UniProtKB/Swiss-Prot CatalyticActivity: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
UniProtKB/Swiss-Prot Function: Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.

Enzyme Numbers (IUBMB) for GNMT Gene

Gene Ontology (GO) - Molecular Function for GNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0005542 folic acid binding IEA --
GO:0008168 methyltransferase activity --
GO:0016594 glycine binding IDA 15340920
GO:0017174 glycine N-methyltransferase activity IDA 15340920
genes like me logo Genes that share ontologies with GNMT: view
genes like me logo Genes that share phenotypes with GNMT: view

Animal Models for GNMT Gene

MGI Knock Outs for GNMT:

miRNA for GNMT Gene

miRTarBase miRNAs that target GNMT

No data available for Transcription Factor Targeting and HOMER Transcription for GNMT Gene

Localization for GNMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for GNMT Gene


Subcellular locations from

Jensen Localization Image for GNMT Gene COMPARTMENTS Subcellular localization image for GNMT gene
Compartment Confidence
cytosol 3
nucleus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for GNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with GNMT: view

Pathways for GNMT Gene

genes like me logo Genes that share pathways with GNMT: view

Pathways by source for GNMT Gene

1 KEGG pathway for GNMT Gene

Gene Ontology (GO) - Biological Process for GNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005977 glycogen metabolic process IEA --
GO:0006111 regulation of gluconeogenesis IEA --
GO:0006464 cellular protein modification process NAS 10843803
GO:0006555 methionine metabolic process IEA --
GO:0006730 one-carbon metabolic process IEA --
genes like me logo Genes that share ontologies with GNMT: view

Compounds for GNMT Gene

(5) HMDB Compounds for GNMT Gene

Compound Synonyms Cas Number PubMed IDs
Folic acid
  • Acifolic
  • 2-Aminoacetate
  • (S)-5'-(S)-(3-Amino-3-carboxypropyl)-5'-thioadenosine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • (Methylamino)acetate

(4) Drugbank Compounds for GNMT Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Citric Acid
77-92-9 target
  • 2-Aminoacetic acid
56-40-6 target
979-92-0 target
  • Acylcarnitine
29908-03-0 target cofactor

(9) Novoseek inferred chemical compound relationships for GNMT Gene

Compound -log(P) Hits PubMed IDs
sarcosine 88.5 6
s-adenosylmethionine 87.5 30
s-adenosylhomocysteine 87 18
cystathionine 76.2 2
methionine 71.9 13
genes like me logo Genes that share compounds with GNMT: view

Transcripts for GNMT Gene

mRNA/cDNA for GNMT Gene

Unigene Clusters for GNMT Gene

Glycine N-methyltransferase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for GNMT Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5

Relevant External Links for GNMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GNMT Gene

mRNA expression in normal human tissues for GNMT Gene

mRNA differential expression in normal tissues according to GTEx for GNMT Gene

This gene is overexpressed in Pancreas (33.5) and Liver (10.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for GNMT Gene

SOURCE GeneReport for Unigene cluster for GNMT Gene Hs.144914

mRNA Expression by UniProt/SwissProt for GNMT Gene

Tissue specificity: Abundant in liver
genes like me logo Genes that share expressions with GNMT: view

Orthologs for GNMT Gene

This gene was present in the common ancestor of animals.

Orthologs for GNMT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GNMT 36
  • 99.66 (n)
  • 100 (a)
  • 100 (a)
(Bos Taurus)
Mammalia GNMT 36
  • 90.82 (n)
  • 92.86 (a)
  • 92 (a)
(Canis familiaris)
Mammalia GNMT 36
  • 92.66 (n)
  • 96.27 (a)
  • 76 (a)
(Mus musculus)
Mammalia Gnmt 36
  • 88.05 (n)
  • 92.15 (a)
Gnmt 16
Gnmt 37
  • 92 (a)
(Monodelphis domestica)
Mammalia GNMT 37
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 67 (a)
-- 37
  • 80 (a)
(Gallus gallus)
Aves GNMT 37
  • 78 (a)
(Anolis carolinensis)
Reptilia GNMT 37
  • 80 (a)
(Danio rerio)
Actinopterygii gnmt 36
  • 69.41 (n)
  • 73.29 (a)
gnmt 37
  • 73 (a)
wufb02g11 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002198 36
  • 61.57 (n)
  • 59.43 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6188 36
  • 63.46 (n)
  • 59.07 (a)
CG6188 37
  • 57 (a)
CG6188 38
  • 57 (a)
Species with no ortholog for GNMT:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for GNMT Gene

Gene Tree for GNMT (if available)
Gene Tree for GNMT (if available)

Paralogs for GNMT Gene

No data available for Paralogs for GNMT Gene

Variants for GNMT Gene

Sequence variations from dbSNP and Humsavar for GNMT Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs2296805 -- 42,961,020(+) GTCTG(G/T)CTCAG intron-variant
rs3800292 -- 42,962,571(+) GAAAA(A/G)CCCAT intron-variant
rs5031030 -- 42,961,014(+) ATCGG(A/G)GTCTG intron-variant
rs7759302 -- 42,961,514(+) GGCCC(G/T)GGTTG intron-variant
rs7760250 -- 42,962,101(+) GCAGA(A/G)GAACG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GNMT Gene

Variant ID Type Subtype PubMed ID
nsv830651 CNV Loss 17160897
nsv462927 CNV Loss 19166990

Relevant External Links for GNMT Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

Disorders for GNMT Gene

(1) OMIM Diseases for GNMT Gene (606628)


  • Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664]: The only clinical abnormalities in patients with this deficiency are mild hepatomegaly and chronic elevation of serum transaminases. {ECO:0000269 PubMed:11810299, ECO:0000269 PubMed:14739680}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for GNMT Gene

(5) Novoseek inferred disease relationships for GNMT Gene

Disease -log(P) Hits PubMed IDs
gnmt deficiency 97.7 9
hepatocellular carcinoma 55.7 7
hepatomegaly 50.5 1
liver diseases 35.1 1
tumors 0 10

Relevant External Links for GNMT

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with GNMT: view

Publications for GNMT Gene

  1. Characterization of glycine-N-methyltransferase-gene expression in human hepatocellular carcinoma. (PMID: 9495250) Chen Y.-M.A. … Chen P.H. (Int. J. Cancer 1998) 2 3 4 23
  2. Genomic structure, expression, and chromosomal localization of the human glycine N-methyltransferase gene. (PMID: 10843803) Chen Y.-M.A. … Yang-Feng T.L. (Genomics 2000) 2 3 4 23
  3. Mutations in human glycine N-methyltransferase give insights into its role in methionine metabolism. (PMID: 11810299) Luka Z. … Wagner C. (Hum. Genet. 2002) 3 4 23 25
  4. Effect of naturally occurring mutations in human glycine N- methyltransferase on activity and conformation. (PMID: 14651980) Luka Z. … Wagner C. (Biochem. Biophys. Res. Commun. 2003) 3 4 23
  5. Glycine N-methyltransferase deficiency: a new patient with a novel mutation. (PMID: 14739680) Augoustides-Savvopoulou P. … Mudd S.H. (J. Inherit. Metab. Dis. 2003) 3 4 23

Products for GNMT Gene

Sources for GNMT Gene

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