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... See more...

Aliases for GNMT Gene

Aliases for GNMT Gene

  • Glycine N-Methyltransferase 2 3 4 5
  • EC 2.1.1.20 4 52
  • 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
  • GC06P042960
  • GC06P043271
  • GC06P043281
  • GC06P043430
  • GC06P042961
  • GC06P043255

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 Viral mRNA Translation and Metabolism. Gene Ontology (GO) annotations related to this gene include methyltransferase activity and folic acid binding.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J042928 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.4 -8.8 -8811 6 FOXK2 ZBTB40 ZNF217 ZSCAN5C SIN3A NRF1 TCF12 MYC POLR2G USF1 CNPY3 5MWI_A-162 ENSG00000287825 piR-40685 GNMT PEX6 ZNF318 PPP2R5D RPL24P4 POLH
GH06J042959 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 500.4 +21.2 21186 2 POLR2G POLR2A ZBTB26 TGIF2 CTBP1 SIN3A KLF9 SRSF1 CEBPB SP2 lnc-PEX6-2 GNMT PEX6 CUL7 RPL24P4 RF00017-5554
GH06J042938 Enhancer 1.1 ENCODE dbSUPER 507.4 +0.3 264 1.4 EP300 FOXK2 USF1 NCOR1 KDM6A FOXA1 ZBTB25 TGIF2 SKI TBX3 GNMT ENSG00000231113 PEX6 NONHSAG043795.2 CNPY3
GH06J042040 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 5.6 -893.0 -892987 11.1 RXRA EP300 FOXK2 HNRNPK ZBTB40 ZNF217 CTCF SIN3A NRF1 TCF12 CCND3 TAF8 ENSG00000124593 RNU6-761P ENSG00000207371 MED20 BYSL FRS3 PRICKLE4 USP49
GH06J042977 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 4.7 +39.4 39389 4 ZBTB40 EP300 NRF1 POLR2G GTF2E2 PHF8 ZFX ZNF639 ZNF10 ZIC2 PEX6 ZNF318 POLH GTPBP2 CUL7 ENSG00000219470 ABCC10 XPO5 POLR1C RRP36
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GNMT on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GNMT

Top Transcription factor binding sites by QIAGEN in the GNMT gene promoter:
  • C/EBPalpha
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • LCR-F1
  • Nkx2-5
  • Pax-5

Genomic Locations for GNMT Gene

Genomic Locations for GNMT Gene
chr6:42,939,415-42,963,880
(GRCh38/hg38)
Size:
24,466 bases
Orientation:
Plus strand
chr6:42,928,496-42,931,618
(GRCh37/hg19)
Size:
3,123 bases
Orientation:
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:
    Q14749-GNMT_HUMAN
    Recommended name:
    Glycine N-methyltransferase
    Protein Accession:
    Q14749
    Secondary Accessions:
    • Q5T8W2
    • Q9NNZ1
    • Q9NS24

    Protein attributes for GNMT Gene

    Size:
    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

Q14749:
  • GGLLVIDHRNYD
  • PCYFIHVL
  • SVDASDKMLKYALKERWNRR
  • WLLGLLRQHGC
  • WVIEEANW
  • RVLDVACGTGVDSIMLVEEGFSV
  • GDQSEHRLALKNI

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

HGNC:
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:
  • Glycine N-methyltransferase (GNMT_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q14749

UniProtKB/Swiss-Prot:

GNMT_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Glycine N-methyltransferase family.
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 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=glycine + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + sarcosine; Xref=Rhea:RHEA:19937, ChEBI:CHEBI:15378, ChEBI:CHEBI:57305, ChEBI:CHEBI:57433, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789; EC=2.1.1.20;.

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:

Animal Model Products

CRISPR Products

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

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 3
extracellular 2
mitochondrion 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
lysosome 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 IBA 21873635
GO:0006464 cellular protein modification process NAS 10843803
GO:0006555 methionine metabolic process IEA --
GO:0006730 one-carbon metabolic process IBA,IEA 21873635
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

(10) 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 1480
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 369
Ademetionine Approved, Investigational Nutra Target, cofactor 0
Mercaptopurine Approved Pharma 228
Folic acid Approved, Vet_approved Nutra 4724

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with GNMT: view

Transcripts for GNMT Gene

mRNA/cDNA for GNMT Gene

2 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5
SP1:
SP2:

Relevant External Links for GNMT Gene

GeneLoc Exon Structure for
GNMT

Expression for GNMT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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 and MOPED for GNMT Gene



Protein tissue co-expression partners for GNMT Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GNMT

SOURCE GeneReport for Unigene cluster for GNMT Gene:

Hs.144914

mRNA Expression by UniProt/SwissProt for GNMT Gene:

Q14749-GNMT_HUMAN
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
Systems:
  • digestive
Regions:
Abdomen:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia GNMT 31 30
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GNMT 31 30
  • 92.66 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GNMT 31 30
  • 90.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gnmt 17 31 30
  • 88.05 (n)
oppossum
(Monodelphis domestica)
Mammalia GNMT 31
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 80 (a)
OneToMany
-- 31
  • 67 (a)
OneToMany
chicken
(Gallus gallus)
Aves GNMT 31
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GNMT 31
  • 80 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii gnmt 31 30
  • 69.41 (n)
OneToOne
wufb02g11 30
fruit fly
(Drosophila melanogaster)
Insecta CG6188 31 32 30
  • 63.46 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002198 30
  • 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

ENSEMBL:
Gene Tree for GNMT (if available)
TreeFam:
Gene Tree for GNMT (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GNMT: view image

Paralogs for GNMT Gene

No data available for Paralogs for GNMT Gene

Variants for GNMT Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GNMT Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
712933 Benign: not provided 42,963,139(+) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
724869 Likely Benign: not provided 42,962,317(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,INTRON_VARIANT
749919 Likely Benign: not provided 42,960,956(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,INTRON_VARIANT
779912 Benign: not provided 42,962,838(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs121907888 Pathogenic: Glycine N-methyltransferase deficiency. Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,960,916(+) T/Cp.Leu50Pro MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for GNMT Gene

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)
GNMT
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GNMT

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

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

- elite association - COSMIC cancer census association via MalaCards
Search GNMT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GNMT_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 54
  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 23 54
  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 23 54
  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 23 41 54
  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 23 41 54

Products for GNMT Gene

Sources for GNMT Gene