GNMT (glycine N-methyltransferase)

Gene

• Entrez ID: 27232
• Gene name: Glycine N-methyltransferase
• Gene symbol: GNMT
• Synonyms (NCBI Gene): HEL-S-182mP
• Chromosome: 6
• Chromosome location: 6p21.1
• 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016781	hsa-miR-335-5p	Microarray	18185580
MIRT2437451	hsa-miR-1291	CLIP-seq
MIRT2437452	hsa-miR-3151	CLIP-seq
MIRT2437453	hsa-miR-328	CLIP-seq
MIRT2437454	hsa-miR-3650	CLIP-seq
MIRT2437455	hsa-miR-4283	CLIP-seq
MIRT2437456	hsa-miR-4447	CLIP-seq
MIRT2437457	hsa-miR-4472	CLIP-seq
MIRT2437458	hsa-miR-4489	CLIP-seq
MIRT2437459	hsa-miR-485-5p	CLIP-seq
MIRT2437460	hsa-miR-491-5p	CLIP-seq
MIRT2437451	hsa-miR-1291	CLIP-seq
MIRT2437452	hsa-miR-3151	CLIP-seq
MIRT2437453	hsa-miR-328	CLIP-seq
MIRT2437454	hsa-miR-3650	CLIP-seq
MIRT2437455	hsa-miR-4283	CLIP-seq
MIRT2437456	hsa-miR-4447	CLIP-seq
MIRT2437457	hsa-miR-4472	CLIP-seq
MIRT2437458	hsa-miR-4489	CLIP-seq
MIRT2437459	hsa-miR-485-5p	CLIP-seq
MIRT2437460	hsa-miR-491-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
AR	Unknown	23997240

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16189514, 21988832, 26871637, 31515488, 32296183
GO:0005542	Function	Folic acid binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0006111	Process	Regulation of gluconeogenesis	IBA
GO:0006111	Process	Regulation of gluconeogenesis	IEA
GO:0006555	Process	Methionine metabolic process	IEA
GO:0006730	Process	One-carbon metabolic process	IBA
GO:0006730	Process	One-carbon metabolic process	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0016594	Function	Glycine binding	IBA
GO:0016594	Function	Glycine binding	IDA	15340920
GO:0016594	Function	Glycine binding	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0017174	Function	Glycine N-methyltransferase activity	IBA
GO:0017174	Function	Glycine N-methyltransferase activity	IDA	15340920
GO:0017174	Function	Glycine N-methyltransferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0042802	Function	Identical protein binding	IBA
GO:0042802	Function	Identical protein binding	IPI	16189514, 25502805, 26871637, 31515488
GO:0046498	Process	S-adenosylhomocysteine metabolic process	IBA
GO:0046500	Process	S-adenosylmethionine metabolic process	IBA
GO:0046500	Process	S-adenosylmethionine metabolic process	IDA	15340920
GO:0046500	Process	S-adenosylmethionine metabolic process	IEA
GO:0051289	Process	Protein homotetramerization	IBA
GO:0051289	Process	Protein homotetramerization	IEA
GO:0051289	Process	Protein homotetramerization	IPI	15340920
GO:1901052	Process	Sarcosine metabolic process	IBA
GO:1904047	Function	S-adenosyl-L-methionine binding	IBA

Other IDs

• MIM: 606628
• HGNC: 4415
• e!Ensembl: ENSG00000124713

Protein

• UniProt ID: Q14749
• Protein name: Glycine N-methyltransferase (EC 2.1.1.20)
• Protein function: Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy), a reaction regulated by the binding of 5-methyltetrahydrofolate.
• PDB: 1R74, 2AZT
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13649	Methyltransf_25	61 → 171	Methyltransferase domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed only in liver, pancreas, and prostate. {ECO:0000269|PubMed:9495250}.
• Sequence:

  MVDSVYRTRSLGVAAEGLPDQYADGEAARVWQLYIGDTRSRTAEYKAWLLGLLRQHGCQR
  VLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRHEPAFDKWVIEEANWMT
  LDKDVPQSAEGGFDAVICLGNSFAHLPDCKGDQSEHRLALKNIASMVRAGGLLVIDHRNY
  DHILSTGCAPPGKNIYYKSDLTKDVTTSVLIVNNKAHMVTLDYTVQVPGAGQDGSPGLSK
  FRLSYYPHCLASFTELLQAAFGGKCQHSVLGDFKPYKPGQTYIPCYFIHVLKRTD

• Sequence length: 295

Pathways

KEGG:

Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
One carbon pool by folate
Metabolic pathways

Reactome:

Glyoxylate metabolism and glycine degradation

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Glycine N-methyltransferase deficiency	Pathogenic	rs121907888, rs864321678	RCV000004386 RCV000203283

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs4987174	RCV005923539
Familial cancer of breast	Benign	rs2296804	RCV005909633
Familial pancreatic carcinoma	Benign	rs4987174	RCV005923543
GNMT-related disorder	Likely benign; Benign	rs143043221, rs370044528, rs535188125	RCV003920952 RCV003921142 RCV003933596
Hepatocellular carcinoma	Benign	rs2296804, rs4987174	RCV005909634 RCV005923540
Nonpapillary renal cell carcinoma	Benign	rs4987174	RCV005923541
Ovarian cancer	Benign	rs4987174	RCV005923542
Ovarian serous cystadenocarcinoma	Likely benign	rs370454543	RCV005931531
Thymoma	Benign	rs4987174	RCV005923544

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma of Lung	Associate	37589509
Breast Neoplasms	Associate	24884785, 37747033
Carcinogenesis	Associate	21572396
Carcinoma Hepatocellular	Associate	21411609, 30138348, 32290267, 35008908
Dysplastic Nevus Syndrome	Associate	24999589
Heart Defects Congenital	Associate	28264803
Liver Diseases	Associate	30138348
Melanoma	Associate	24999589
Neoplasm Metastasis	Associate	25550822
Neoplasms	Inhibit	21411609
Neoplasms	Associate	21572396, 23883094
Oropharyngeal Neoplasms	Associate	32415241
Pancreatic Neoplasms	Associate	31706267
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	21790528
Prostatic Neoplasms	Associate	19212411, 21572396, 23883094, 23997240, 24800880, 28033303
Visceral myopathy familial external ophthalmoplegia	Associate	22137549