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Aliases for DMGDH Gene

Aliases for DMGDH Gene

  • Dimethylglycine Dehydrogenase 2 3 5
  • ME2GLYDH 3 4
  • Dimethylglycine Dehydrogenase, Mitochondrial 3
  • EC 1.5.8.4 4
  • DMGDHD 3

External Ids for DMGDH Gene

Previous GeneCards Identifiers for DMGDH Gene

  • GC05M077099
  • GC05M078530
  • GC05M078332
  • GC05M078377
  • GC05M078329
  • GC05M073499
  • GC05M078293

Summaries for DMGDH Gene

Entrez Gene Summary for DMGDH Gene

  • 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 as cofactors. Mutation in this gene causes dimethylglycine dehydrogenase deficiency, characterized by a fishlike body odor, chronic muscle fatigue, and elevated levels of the muscle form of creatine kinase in serum. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

GeneCards Summary for DMGDH Gene

DMGDH (Dimethylglycine Dehydrogenase) is a Protein Coding gene. Diseases associated with DMGDH include Dimethylglycine Dehydrogenase Deficiency and Sarcosinemia. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. Gene Ontology (GO) annotations related to this gene include electron transfer activity. An important paralog of this gene is SARDH.

UniProtKB/Swiss-Prot for DMGDH Gene

  • Catalyzes the demethylation of N,N-dimethylglycine to sarcosine. Also has activity with sarcosine in vitro.

Additional gene information for DMGDH Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DMGDH Gene

Genomics for DMGDH Gene

GeneHancer (GH) Regulatory Elements for DMGDH Gene

Promoters and enhancers for DMGDH 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
GH05I079234 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 562.2 -1.0 -1026 4.3 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 ZNF2 IRF4 YY1 POLR2B DMGDH JMY BHMT GC05M079243
GH05I079069 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 550.1 +166.1 166086 1.5 SAP130 BACH1 KMT2B ZNF48 YY1 ZNF316 POLR2A EGR1 NFE2 MAFK BHMT2 DMGDH BHMT
GH05I078359 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.7 +875.3 875342 3.3 ARNT ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 SCAMP1 SCAMP1-AS1 PIR62844 JMY RPL7P23 RPS3AP20 DMGDH PIR51536
GH05I079261 Enhancer 0.4 ENCODE 24.2 -25.7 -25657 1.2 SCRT2 RUNX3 DMGDH JMY GC05M079243 GC05M079285
GH05I079318 Enhancer 0.9 Ensembl ENCODE 8.6 -83.4 -83367 1.7 HDAC1 LEF1 BACH1 CEBPG ZBTB40 IRF9 FOSL1 CTBP1 POLR2A TRIM24 BHMT DMGDH BHMT2 LOC102724530 RPS3AP20 JMY
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DMGDH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DMGDH gene promoter:

Genomic Locations for DMGDH Gene

Genomic Locations for DMGDH Gene
chr5:78,997,564-79,236,038
(GRCh38/hg38)
Size:
238,475 bases
Orientation:
Minus strand
chr5:78,293,429-78,531,861
(GRCh37/hg19)

Genomic View for DMGDH Gene

Genes around DMGDH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DMGDH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DMGDH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DMGDH Gene

Proteins for DMGDH Gene

  • Protein details for DMGDH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UI17-M2GD_HUMAN
    Recommended name:
    Dimethylglycine dehydrogenase, mitochondrial
    Protein Accession:
    Q9UI17
    Secondary Accessions:
    • B2RBN0
    • B4E1J9

    Protein attributes for DMGDH Gene

    Size:
    866 amino acids
    Molecular mass:
    96811 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for DMGDH Gene

    Alternative splice isoforms for DMGDH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DMGDH Gene

Post-translational modifications for DMGDH Gene

No Post-translational modifications

No data available for DME Specific Peptides for DMGDH Gene

Domains & Families for DMGDH Gene

Gene Families for DMGDH Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q9UI17

UniProtKB/Swiss-Prot:

M2GD_HUMAN :
  • Belongs to the GcvT family.
Family:
  • Belongs to the GcvT family.
genes like me logo Genes that share domains with DMGDH: view

Function for DMGDH Gene

Molecular function for DMGDH Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.4 mM for N,N-dimethylglycine {ECO:0000269 PubMed:27486859}; Vmax=22.1 umol/min/mg enzyme; Note=kcat is 213 min(-1) for N,N-dimethylglycine. {ECO:0000269 PubMed:27486859};
UniProtKB/Swiss-Prot CatalyticActivity:
N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein.
UniProtKB/Swiss-Prot Function:
Catalyzes the demethylation of N,N-dimethylglycine to sarcosine. Also has activity with sarcosine in vitro.

Enzyme Numbers (IUBMB) for DMGDH Gene

Phenotypes From GWAS Catalog for DMGDH Gene

Gene Ontology (GO) - Molecular Function for DMGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0009055 electron transfer activity NAS 10767172
GO:0016491 oxidoreductase activity IEA --
GO:0047865 dimethylglycine dehydrogenase activity TAS --
genes like me logo Genes that share ontologies with DMGDH: view
genes like me logo Genes that share phenotypes with DMGDH: view

Human Phenotype Ontology for DMGDH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DMGDH Gene

MGI Knock Outs for DMGDH:

Animal Model Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for DMGDH Gene

Localization for DMGDH Gene

Subcellular locations from UniProtKB/Swiss-Prot for DMGDH Gene

Mitochondrion.

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 DMGDH gene
Compartment Confidence
mitochondrion 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for DMGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix IBA,TAS --
genes like me logo Genes that share ontologies with DMGDH: view

Pathways & Interactions for DMGDH Gene

genes like me logo Genes that share pathways with DMGDH: view

UniProtKB/Swiss-Prot Q9UI17-M2GD_HUMAN

  • Pathway: Amine and polyamine degradation; betaine degradation; sarcosine from betaine: step 2/2.

Gene Ontology (GO) - Biological Process for DMGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006579 amino-acid betaine catabolic process IEA --
GO:0019695 choline metabolic process NAS 10767172
GO:0022900 electron transport chain IEA --
GO:0042426 choline catabolic process IMP,TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with DMGDH: view

No data available for SIGNOR curated interactions for DMGDH Gene

Drugs & Compounds for DMGDH Gene

(10) Drugs for DMGDH Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Formaldehyde Approved, Vet_approved Pharma 102
FAD Approved Pharma 0
Water Approved Pharma 0
spermine Approved Nutra Full agonist, Agonist 0
dimethylglycine Experimental Pharma 0

(3) Additional Compounds for DMGDH Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N1-acetylspermine
  • N'-Acetylspermine
  • N'-Monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-Acetamide
  • N-Acetylspermine
25593-72-0
Norspermidine
  • -1,3-propanediamine
  • 1,7-Diamino-4-azaheptane
  • 3, 3'-Diaminodipropylamine
  • 3, {3'-Iminobis[propylamine]}
  • 3,3'-Diamino-Dipropylamine
56-18-8
genes like me logo Genes that share compounds with DMGDH: view

Transcripts for DMGDH Gene

Unigene Clusters for DMGDH Gene

Dimethylglycine dehydrogenase:
Representative Sequences:

Clone Products

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

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18
SP1: - -
SP2: -
SP3: -
SP4:

Relevant External Links for DMGDH Gene

GeneLoc Exon Structure for
DMGDH
ECgene alternative splicing isoforms for
DMGDH

Expression for DMGDH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DMGDH Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DMGDH Gene

This gene is overexpressed in Liver (x22.1) and Kidney - Cortex (x9.3).

Protein differential expression in normal tissues from HIPED for DMGDH Gene

This gene is overexpressed in Liver, secretome (46.5) and Liver (16.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for DMGDH Gene



Protein tissue co-expression partners for DMGDH Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DMGDH Gene:

DMGDH

SOURCE GeneReport for Unigene cluster for DMGDH Gene:

Hs.655653

Evidence on tissue expression from TISSUES for DMGDH Gene

  • Liver(4.6)
  • Kidney(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for DMGDH Gene

Germ Layers:
  • mesoderm
Systems:
  • skeletal muscle
genes like me logo Genes that share expression patterns with DMGDH: view

No data available for mRNA Expression by UniProt/SwissProt for DMGDH Gene

Orthologs for DMGDH Gene

This gene was present in the common ancestor of animals.

Orthologs for DMGDH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DMGDH 33 34
  • 99.54 (n)
cow
(Bos Taurus)
Mammalia DMGDH 33 34
  • 91.64 (n)
dog
(Canis familiaris)
Mammalia DMGDH 33 34
  • 90.65 (n)
rat
(Rattus norvegicus)
Mammalia Dmgdh 33
  • 86.14 (n)
mouse
(Mus musculus)
Mammalia Dmgdh 33 16 34
  • 85.86 (n)
oppossum
(Monodelphis domestica)
Mammalia DMGDH 34
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DMGDH 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves DMGDH 33 34
  • 77.19 (n)
lizard
(Anolis carolinensis)
Reptilia DMGDH 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia dmgdh 33
  • 73.9 (n)
zebrafish
(Danio rerio)
Actinopterygii dmgdh 33 34
  • 66.83 (n)
Dr.5571 33
worm
(Caenorhabditis elegans)
Secernentea Y37E3.17 35 33 34
  • 48.13 (n)
Y106G6H.5 35
  • 26 (a)
Species where no ortholog for DMGDH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for DMGDH Gene

ENSEMBL:
Gene Tree for DMGDH (if available)
TreeFam:
Gene Tree for DMGDH (if available)

Paralogs for DMGDH Gene

Paralogs for DMGDH Gene

(2) SIMAP similar genes for DMGDH Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with DMGDH: view

Variants for DMGDH Gene

Sequence variations from dbSNP and Humsavar for DMGDH Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs121908331 pathogenic, likely-pathogenic, Dimethylglycine dehydrogenase deficiency, not provided, DMGDH deficiency (DMGDHD) [MIM:605850] 79,055,859(-) T/C coding_sequence_variant, intron_variant, missense_variant
rs200216040 uncertain-significance, Dimethylglycine dehydrogenase deficiency 79,044,442(-) G/A coding_sequence_variant, intron_variant, non_coding_transcript_variant, stop_gained
rs56774046 likely-pathogenic, not provided 79,069,518(-) A/G splice_donor_variant
rs1057521498 likely-benign, not specified 79,051,354(-) T/C coding_sequence_variant, intron_variant, synonymous_variant
rs1057522402 likely-benign, not specified 79,055,849(-) G/A coding_sequence_variant, intron_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for DMGDH Gene

Variant ID Type Subtype PubMed ID
esv2762527 CNV gain 21179565
nsv1022839 CNV gain 25217958
nsv462215 CNV gain 19166990
nsv462216 CNV loss 19166990
nsv519156 CNV gain 19592680
nsv598740 CNV gain 21841781
nsv598741 CNV loss 21841781

Variation tolerance for DMGDH Gene

Residual Variation Intolerance Score: 58.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.75; 95.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DMGDH Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DMGDH Gene

Disorders for DMGDH Gene

MalaCards: The human disease database

(2) MalaCards diseases for DMGDH Gene - From: HGMD, OMIM, GTR, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
dimethylglycine dehydrogenase deficiency
  • dmgdhd
sarcosinemia
  • sarcos
- elite association - COSMIC cancer census association via MalaCards
Search DMGDH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

M2GD_HUMAN
  • DMGDH deficiency (DMGDHD) [MIM:605850]: Disorder characterized by fish odor, muscle fatigue with increased serum creatine kinase. Biochemically it is characterized by an increase of N,N-dimethylglycine (DMG) in serum and urine. {ECO:0000269 PubMed:11231903, ECO:0000269 PubMed:27486859}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for DMGDH

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 DMGDH: view

No data available for Genatlas for DMGDH Gene

Publications for DMGDH Gene

  1. Cloning of dimethylglycine dehydrogenase and a new human inborn error of metabolism, dimethylglycine dehydrogenase deficiency. (PMID: 11231903) Binzak BA … Vockley J (American journal of human genetics 2001) 2 3 4 22 58
  2. Structure and analysis of the human dimethylglycine dehydrogenase gene. (PMID: 10767172) Binzak BA … Vockley J (Molecular genetics and metabolism 2000) 2 3 4 22 58
  3. Defect in dimethylglycine dehydrogenase, a new inborn error of metabolism: NMR spectroscopy study. (PMID: 10102904) Moolenaar SH … Wevers RA (Clinical chemistry 1999) 3 4 22 58
  4. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. (PMID: 27486859) Augustin P … Macheroux P (The FEBS journal 2016) 3 4 58
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58

Products for DMGDH Gene

Sources for DMGDH Gene

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