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Aliases for GNMT Gene

Aliases for GNMT Gene

  • Glycine N-Methyltransferase 2 3 5
  • EC 2.1.1.20 4 58
  • 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 Metabolism and Viral mRNA Translation. 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

Regulatory Elements for GNMT Gene

Enhancers for GNMT Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H042040 2 FANTOM5 Ensembl ENCODE dbSUPER 5.6 -893.1 -893087 10 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D SSRP1 ENSG00000124593 CCND3 RNU6-761P MED20 ENSG00000207371 BYSL FRS3 PRICKLE4 USP49 TOMM6
GH06H042938 1.2 ENCODE dbSUPER 7.5 +0.3 264 1 FOXA2 MLX ARID4B DMAP1 YY1 SLC30A9 SP5 ZHX2 MXD4 NFYC PEX6 GNMT ENSG00000231113
GH06H042769 1.8 FANTOM5 Ensembl ENCODE dbSUPER 4.7 -168.0 -168002 2 HDGF PKNOX1 ZNF143 ZNF207 ATF7 ETV6 RUNX3 CREM IKZF2 SMARCA5 TBCC CUL7 RPL7L1 CUL9 ABCC10 TRERF1 C6orf226 PRPH2 BICRAL GNMT
GH06H042977 1.1 ENCODE 4.7 +39.9 39926 2 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 PEX6 ZNF318 POLH RRP36 GTPBP2 RPL34P14 XPO5 RPS2P29 POLR1C ABCC10
GH06H043266 2 FANTOM5 Ensembl ENCODE dbSUPER 2.2 +334.0 334038 13 FOXA2 MLX ARNT ZFP64 ARID4B DMAP1 YY1 SLC30A9 ZNF143 PAF1 POLH ZNF318 GTPBP2 POLR1C RPS2P29 ABCC10 XPO5 CUL7 UBR2 RRP36
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GNMT on UCSC Golden Path with GeneCards custom track

Genomic Location for GNMT Gene

Chromosome:
6
Start:
42,939,415 bp from pter
End:
42,963,880 bp from pter
Size:
24,466 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:

Antibody Products

  • R&D Systems Antibodies for GNMT (Glycine N-Methyltransferase/GNMT)
  • Santa Cruz Biotechnology (SCBT) Antibodies for GNMT

Protein Products

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:

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 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:

Animal Model Products

CRISPR Products

miRNA for GNMT Gene

miRTarBase miRNAs that target GNMT

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GNMT
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 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
Glycine Approved, Vet_approved Nutra Full agonist, Agonist, Target 243
Ademetionine Approved Nutra Target, cofactor 0
Mercaptopurine Approved Pharma 0
Folic Acid Approved, Vet_approved Nutra 4513
s-adenosylhomocysteine Experimental Pharma Target 0

(5) 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
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GNMT
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
GNMT

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:

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
Organs:
Abdomen:
  • liver
genes like me logo Genes that share expression patterns with GNMT: view

Primer Products

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 33 34
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia GNMT 33 34
  • 92.66 (n)
cow
(Bos Taurus)
Mammalia GNMT 33 34
  • 90.82 (n)
mouse
(Mus musculus)
Mammalia Gnmt 33 16 34
  • 88.05 (n)
oppossum
(Monodelphis domestica)
Mammalia GNMT 34
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 80 (a)
OneToMany
-- 34
  • 67 (a)
OneToMany
chicken
(Gallus gallus)
Aves GNMT 34
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GNMT 34
  • 80 (a)
OneToOne
zebrafish
(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

ENSEMBL:
Gene Tree for GNMT (if available)
TreeFam:
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
rs121907888 Pathogenic, Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,960,916(+) GCTGC(C/T)TGGGC intron-variant, nc-transcript-variant, reference, missense
rs121907889 Pathogenic, Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,963,149(+) TTGAT(A/C)ATCGC intron-variant, reference, missense
rs864321678 Pathogenic, Glycine N-methyltransferase deficiency (GNMT deficiency) [MIM:606664] 42,962,849(+) TGGAA(A/G)CAGTT nc-transcript-variant, reference, missense
rs736158 Likely benign 42,964,016(+) GGGGC(A/G)GGACA nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1051218 Uncertain significance 42,964,123(-) CAGGC(C/T)GGCTC nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime

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)

Relevant External Links for GNMT Gene

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

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, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
glycine n-methyltransferase deficiency
  • gnmt deficiency
hypermethioninemia
  • deficiency of methionine adenosyltransferase
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
- 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.

Relevant External Links for GNMT

Genetic Association Database (GAD)
GNMT
Human Genome Epidemiology (HuGE) Navigator
GNMT
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GNMT
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 60
  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 60
  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 60
  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 45 60
  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 45 60

Products for GNMT Gene

Sources for GNMT Gene

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