DMGDH (dimethylglycine dehydrogenase)

Gene

• Entrez ID: 29958
• Gene name: Dimethylglycine dehydrogenase
• Gene symbol: DMGDH
• Synonyms (NCBI Gene): DMGDHD, ME2GLYDH
• Chromosome: 5
• Chromosome location: 5q14.1
• Summary: This gene encodes an enzyme involved in the catabolism of choline, catalyzing the oxidative demethylation of dimethylglycine to form sarcosine. The enzyme is found as a monomer in the mitochondrial matrix, and uses flavin adenine dinucleotide and folate a

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908331	T>C	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016761	hsa-miR-335-5p	Microarray	18185580
MIRT021745	hsa-miR-132-3p	Microarray	17612493
MIRT709579	hsa-miR-518e-3p	HITS-CLIP	19536157
MIRT709578	hsa-miR-2682-3p	HITS-CLIP	19536157
MIRT709577	hsa-miR-6781-3p	HITS-CLIP	19536157
MIRT709576	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT709575	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT709574	hsa-miR-4774-3p	HITS-CLIP	19536157
MIRT709573	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT709579	hsa-miR-518e-3p	HITS-CLIP	19536157
MIRT709578	hsa-miR-2682-3p	HITS-CLIP	19536157
MIRT709577	hsa-miR-6781-3p	HITS-CLIP	19536157
MIRT709576	hsa-miR-1251-3p	HITS-CLIP	19536157
MIRT709575	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT709574	hsa-miR-4774-3p	HITS-CLIP	19536157
MIRT709573	hsa-miR-3152-5p	HITS-CLIP	19536157

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	HDA	22658674
GO:0005737	Component	Cytoplasm	IBA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IBA
GO:0005759	Component	Mitochondrial matrix	NAS	10767172
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006579	Process	Amino-acid betaine catabolic process	IEA
GO:0009055	Function	Electron transfer activity	NAS	10767172
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0019695	Process	Choline metabolic process	IEA
GO:0019695	Process	Choline metabolic process	NAS	10767172
GO:0042426	Process	Choline catabolic process	IMP	10102904
GO:0047865	Function	Dimethylglycine dehydrogenase activity	IBA
GO:0047865	Function	Dimethylglycine dehydrogenase activity	IEA
GO:0047865	Function	Dimethylglycine dehydrogenase activity	IMP	11231903

Other IDs

• MIM: 605849
• HGNC: 24475
• e!Ensembl: ENSG00000132837

Protein

• UniProt ID: Q9UI17
• Protein name: Dimethylglycine dehydrogenase, mitochondrial (EC 1.5.8.4) (ME2GLYDH)
• Protein function: Catalyzes the demethylation of N,N-dimethylglycine to sarcosine. Also has activity with sarcosine in vitro.
• PDB: 5L46
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01266	DAO	51 → 414	FAD dependent oxidoreductase	Domain
  PF16350	FAO_M	417 → 471	FAD dependent oxidoreductase central domain	Family
  PF01571	GCV_T	474 → 745	Aminomethyltransferase folate-binding domain	Domain
  PF08669	GCV_T_C	770 → 848	Glycine cleavage T-protein C-terminal barrel domain	Domain

• Sequence:

  MLRPGAQLLRGLLLRSCPLQGSPGRPRSVCGREGEEKPPLSAETQWKDRAETVIIGGGCV
  GVSLAYHLAKAGMKDVVLLEKSELTAGSTWHAAGLTTYFHPGINLKKIHYDSIKLYEKLE
  EETGQVVGFHQPGSIRLATTPVRVDEFKYQMTRTGWHATEQYLIEPEKIQEMFPLLNMNK
  VLAGLYNPGDGHIDPYSLTMALAAGARKCGALLKYPAPVTSLKARSDGTWDVETPQGSMR
  ANRIVNAAGFWAREVGKMIGLEHPLIPVQHQYVVTSTISEVKALKRELPVLRDLEGSYYL
  RQERDGLLFGPYESQEKMKVQDSWVTNGVPPGFGKELFESDLDRIMEHIKAAMEMVPVLK
  KADIINVVNGPITYSPDILPMVGPHQGVRNYWVAIGFGYGIIHAGGVGKYLSDWILHGEP
  PFDLIELDPNRYGKWTTTQYTEAKARESYGFNNIVGYPKEERFAGRPTQRVSGLYQRLES
  KCSMGFHAGWEQPHWFYKPGQDTQYRPSFRRTNWFEPVGSEYKQVMQRVAVTDLSPFGKF
  NIKGQDSIRLLDHLFANVIPKVGFTNISHMLTPKGRVYAELTVSHQSPGEFLLITGSGSE
  LHDLRWIEEEAVKGGYDVEIKNITDELGVLGVAGPQARKVLQKLTSEDLSDDVFKFLQTK
  SLKVSNIPVTAIRISYTGELGWELYHRREDSVALYDAIMNAGQEEGIDNFGTYAMNALRL
  EKAFRAWGLEMNCDTNPLEAGLEYFVKLNKPADFIGKQALKQIKAKGLKRRLVCLTLATD
  DVDPEGNESIWYNGKVVGNTTSGSYSYSIQKSLAFAYVPVQLSEVGQQVEVELLGKNYPA
  VIIQEPLVLTEPTRNRLQKKGGKDKT

• Sequence length: 866

Pathways

KEGG:

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

Reactome:

Choline catabolism

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Dimethylglycine dehydrogenase deficiency	Likely pathogenic	rs121908331	RCV000005008

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Cervical cancer	Benign	rs146240837	RCV005900055
Cholangiocarcinoma	Benign	rs2272038	RCV005918734
DMGDH-related disorder	Likely benign; Benign	rs773725904, rs192307313, rs75051122, rs200459665, rs929359642, rs899976135, rs367867088, rs877052, rs2303128, rs371689941, rs145258663	RCV003906862 RCV003914101 RCV003943864 RCV003944423 RCV003926971 RCV003964758 RCV003957396 RCV003912690 RCV003972587 RCV003922803 RCV003932557
Hepatocellular carcinoma	Benign	rs2272038	RCV005918732
Lung cancer	Benign	rs2272038	RCV005918735
Thymoma	Benign	rs2272038	RCV005918733

Associations from Text Mining
Disease Name	Relationship Type	References
Carcinoma Hepatocellular	Inhibit	27119355
Cerebral Infarction	Associate	26352407
Diabetes Mellitus	Associate	25795213
Dimethylglycine Dehydrogenase Deficiency	Inhibit	11231903, 27486859
Dimethylglycine Dehydrogenase Deficiency	Associate	11231903, 18937046, 27486859
Fatigue	Associate	11231903
Folate Malabsorption Hereditary	Associate	26880641
Metabolism Inborn Errors	Associate	11231903
Neoplasm Metastasis	Inhibit	27119355
Neoplasms	Associate	26690675
Thyroid Cancer Papillary	Associate	26690675