Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	29958
Gene name	Dimethylglycine dehydrogenase
Gene symbol	DMGDH
Synonyms (NCBI Gene)	DMGDHDME2GLYDH
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

Show/Hide all (1)

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

Show/Hide all (16)

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

Show/Hide all (18)

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

MIM	HGNC	e!Ensembl
605849	24475	ENSG00000132837

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

Interactions

View interactions

	KEGG		Reactome
	Glycine, serine and threonine metabolism One carbon pool by folate Metabolic pathways		Choline catabolism

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Dimethylglycine dehydrogenase deficiency	Likely pathogenic	rs121908331	RCV000005008	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DMGDH-related disorder	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC ULCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	27119355	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	26352407	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	25795213	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	CLINGEN_DG	10102904, 9398858		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	GENOMICS_ENGLAND_DG	11231903, 18937046		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	ORPHANET_DG	11231903		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	UNIPROT_DG	11231903, 27486859		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine dehydrogenase deficiency	Pubtator	11231903, 27486859	Inhibit	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine dehydrogenase deficiency	Pubtator	11231903, 18937046, 27486859	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine dehydrogenase deficiency	Dimethylglycine Dehydrogenase Deficiency	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dimethylglycine Dehydrogenase Deficiency	Dimethylglycine Dehydrogenase Deficiency	CTD_human_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Folate Malabsorption Hereditary	Hereditary folate malabsorption	Pubtator	26880641	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	10102904, 11231903		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	27614103		★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	26690675	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

DMGDH (dimethylglycine dehydrogenase)