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Aliases for GNMT Gene

Aliases for GNMT Gene

  • Glycine N-Methyltransferase 2 3 5
  • EC 4 56
  • Epididymis Secretory Sperm Binding Protein Li 182mP 3
  • HEL-S-182mP 3

External Ids for GNMT Gene

Previous GeneCards Identifiers for GNMT Gene

  • GC06P042930
  • GC06P042975
  • GC06P043037
  • GC06P042928
  • GC06P042645

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. 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]

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. Among its related pathways are Glyoxylate metabolism and glycine degradation and Viral mRNA Translation. Gene Ontology (GO) annotations related to this gene include methyltransferase activity and folic acid binding.

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

Additional gene information for GNMT Gene

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

Genomics for GNMT Gene

GeneHancer (GH) Regulatory Elements for GNMT Gene

Promoters and enhancers for GNMT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I042959 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 550.3 +21.1 21148 1.8 FOXA2 ZFP64 ARID4B SIN3A ZNF48 YY1 SLC30A9 ZNF121 GLIS2 ZNF143 GC06M042961 GNMT PEX6 CUL7 RPL24P4
GH06I042938 Enhancer 1.1 ENCODE dbSUPER 557.5 +0.3 264 1.4 FOXA2 MLX ARID4B DMAP1 ZNF48 YY1 SLC30A9 RXRA SP5 NFYC GNMT ENSG00000231113 PEX6 CNPY3
GH06I042040 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.6 -893.1 -893086 11 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 SP3 CCND3 TAF8 PIR49026 ENSG00000124593 RNU6-761P ENSG00000207371 MED20 BYSL FRS3 PRICKLE4
GH06I042977 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.7 +39.9 39925 2.9 HDGF PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 PEX6 POLH RRP36 GTPBP2 ZNF318 XPO5 RPS2P29 POLR1C ENSG00000271754 DNPH1
GH06I042769 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 4.7 -168.0 -168001 3 HDGF PKNOX1 SIN3A KLF5 ZNF207 ZNF143 ATF7 ETV6 IKZF2 RUNX3 TBCC CUL7 RPL7L1 CUL9 ABCC10 TRERF1 C6orf226 PRPH2 BICRAL GNMT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GNMT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GNMT gene promoter:

Genomic Locations for GNMT Gene

Genomic Locations for GNMT Gene
24,466 bases
Plus strand

Genomic View for GNMT Gene

Genes around GNMT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GNMT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GNMT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Selected DME Specific Peptides for GNMT Gene


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 & Families for GNMT Gene

Gene Families for GNMT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for GNMT Gene

Suggested Antigen Peptide Sequences for GNMT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



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

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

Phenotypes From GWAS Catalog 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 IEA --
GO:0016594 glycine binding IEA,IDA 15340920
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with GNMT: view
genes like me logo Genes that share phenotypes with GNMT: view

Human Phenotype Ontology for GNMT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GNMT Gene

MGI Knock Outs for GNMT:

miRNA for GNMT Gene

Clone Products

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

Localization for GNMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for GNMT Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GNMT gene
Compartment Confidence
cytosol 5
nucleus 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GNMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with GNMT: view

Pathways & Interactions for GNMT Gene

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

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

No data available for SIGNOR curated interactions for GNMT Gene

Drugs & Compounds for GNMT Gene

(9) Drugs for GNMT Gene - From: DrugBank, PharmGKB, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citric Acid Approved, Vet_approved Nutra Agonist, Activator, Target 1243
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 254
Ademetionine Approved, Investigational Nutra Target, cofactor 0
Mercaptopurine Approved Pharma 0
Folic Acid Approved, Vet_approved Nutra 4610

(5) Additional Compounds for GNMT Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
genes like me logo Genes that share compounds with GNMT: view

Transcripts for GNMT Gene

mRNA/cDNA for GNMT Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(366) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GNMT Gene

Glycine N-methyltransferase:
Representative Sequences:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for GNMT Gene

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

This gene is overexpressed in Pancreas (x33.5) and Liver (x10.5).

Protein differential expression in normal tissues from HIPED for GNMT Gene

This gene is overexpressed in Liver (35.2), Liver, secretome (23.3), and Gallbladder (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for GNMT Gene

Protein tissue co-expression partners for GNMT Gene

NURSA nuclear receptor signaling pathways regulating expression of GNMT Gene:


SOURCE GeneReport for Unigene cluster for GNMT Gene:


mRNA Expression by UniProt/SwissProt for GNMT Gene:

Tissue specificity: Abundant in liver.

Evidence on tissue expression from TISSUES for GNMT Gene

  • Liver(4.7)
  • Pancreas(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GNMT Gene

Germ Layers:
  • endoderm
  • digestive
  • liver
genes like me logo Genes that share expression patterns with GNMT: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for GNMT Gene

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 33 34
  • 99.66 (n)
(Canis familiaris)
Mammalia GNMT 33 34
  • 92.66 (n)
(Bos Taurus)
Mammalia GNMT 33 34
  • 90.82 (n)
(Mus musculus)
Mammalia Gnmt 33 16 34
  • 88.05 (n)
(Monodelphis domestica)
Mammalia GNMT 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 80 (a)
-- 34
  • 67 (a)
(Gallus gallus)
Aves GNMT 34
  • 78 (a)
(Anolis carolinensis)
Reptilia GNMT 34
  • 80 (a)
(Danio rerio)
Actinopterygii gnmt 33 34
  • 69.41 (n)
wufb02g11 33
fruit fly
(Drosophila melanogaster)
Insecta CG6188 35 33 34
  • 63.46 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002198 33
  • 61.57 (n)
Species where no ortholog for GNMT was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1051218 uncertain-significance, Zellweger syndrome 42,964,123(+) G/A downstream_transcript_variant
rs115180949 benign, uncertain-significance, likely-benign, not specified, Zellweger syndrome, not provided 42,964,342(+) G/A downstream_transcript_variant
rs121907888 pathogenic, Glycine N-methyltransferase deficiency, Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,960,916(+) T/C coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121907889 pathogenic, Glycine N-methyltransferase deficiency, Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,963,149(+) C/A coding_sequence_variant, intron_variant, missense_variant
rs144286892 benign, Zellweger syndrome 42,963,890(+) TTTATTTAT/TTTAT downstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
esv3576145 CNV gain 25503493
nsv1017398 CNV gain 25217958
nsv462927 CNV loss 19166990
nsv602992 CNV loss 21841781
nsv830651 CNV loss 17160897
nsv969395 CNV duplication 23825009

Variation tolerance for GNMT Gene

Residual Variation Intolerance Score: 57.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GNMT Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GNMT Gene

Disorders for GNMT Gene

MalaCards: The human disease database

(3) MalaCards diseases for GNMT Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
glycine n-methyltransferase deficiency
  • gnmt deficiency
  • mat deficiency
hepatocellular carcinoma
  • hcc
- elite association - COSMIC cancer census association via MalaCards
Search GNMT in MalaCards View complete list of genes associated with diseases


  • 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.

Additional Disease Information for GNMT

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GNMT: view

No data available for Genatlas for GNMT Gene

Publications for GNMT Gene

  1. Genomic structure, expression, and chromosomal localization of the human glycine N-methyltransferase gene. (PMID: 10843803) Chen YM … Yang-Feng TL (Genomics 2000) 2 3 4 22 58
  2. Characterization of glycine-N-methyltransferase-gene expression in human hepatocellular carcinoma. (PMID: 9495250) Chen YM … Chen PH (International journal of cancer 1998) 2 3 4 22 58
  3. Destabilization of human glycine N-methyltransferase by H176N mutation. (PMID: 17660255) Luka Z … Wagner C (Protein science : a publication of the Protein Society 2007) 3 4 22 58
  4. Haplotypes, loss of heterozygosity, and expression levels of glycine N-methyltransferase in prostate cancer. (PMID: 17332283) Huang YC … Chen YM (Clinical cancer research : an official journal of the American Association for Cancer Research 2007) 3 22 44 58
  5. The glycine N-methyltransferase (GNMT) 1289 C->T variant influences plasma total homocysteine concentrations in young women after restricting folate intake. (PMID: 16317120) Beagle B … Caudill MA (The Journal of nutrition 2005) 3 22 44 58

Products for GNMT Gene

Sources for GNMT Gene

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