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DMGDH dimethylglycine dehydrogenase [ Homo sapiens (human) ]

Gene ID: 29958, updated on 26-Jun-2015
Official Symbol
DMGDHprovided by HGNC
Official Full Name
dimethylglycine dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:24475
See related
Ensembl:ENSG00000132837; HPRD:05789; MIM:605849; Vega:OTTHUMG00000108159
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DMGDHD; ME2GLYDH
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 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]
Orthologs
See DMGDH in Epigenomics, MapViewer
Location:
5q14.1
Exon count:
19
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 5 NC_000005.10 (78997564..79069674, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (78293387..78365497, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S3a-like Neighboring gene arylsulfatase B Neighboring gene IMPACT pseudogene Neighboring gene betaine--homocysteine S-methyltransferase 2 Neighboring gene betaine--homocysteine S-methyltransferase

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Dimethylglycine dehydrogenase deficiency
MedGen: C1853892 OMIM: 605850 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
NHGRI GWA Catalog
Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
NHGRI GWA Catalog
Genome-wide association study of selenium concentrations.
NHGRI GWA Catalog
  • Glycine, serine and threonine metabolism, organism-specific biosystem (from KEGG)
    Glycine, serine and threonine metabolism, organism-specific biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Glycine, serine and threonine metabolism, conserved biosystem (from KEGG)
    Glycine, serine and threonine metabolism, conserved biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • glycine betaine degradation, organism-specific biosystem (from BIOCYC)
    glycine betaine degradation, organism-specific biosystemBackground : BETAINE "Glycine betaine" plays an important osmoprotectant role in mammals, protects from several other forms of cellular stress and functions as a methyl group donor . In mammals, gly...
  • glycine betaine degradation II (mammalian), conserved biosystem (from BIOCYC)
    glycine betaine degradation II (mammalian), conserved biosystemBackground |FRAME: BETAINE "Glycine betaine"| plays an important osmoprotectant role in mammals, protects from several other forms of cellular stress and functions as a methyl group donor |CITS: [20...
  • superpathway of choline degradation to L-serine, organism-specific biosystem (from BIOCYC)
    superpathway of choline degradation to L-serine, organism-specific biosystemBackground : CHOLINE "Choline" plays a key role in several pathways and its concentration in vivo is carefully regulated. Choline is an essential nutrient for fetal and brain development. It is invo...

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dimethylglycine dehydrogenase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
electron carrier activity NAS
Non-traceable Author Statement
more info
PubMed 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
amino-acid betaine catabolic process IEA
Inferred from Electronic Annotation
more info
 
choline metabolic process NAS
Non-traceable Author Statement
more info
PubMed 
glycine metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
mitochondrial matrix NAS
Non-traceable Author Statement
more info
PubMed 
Preferred Names
dimethylglycine dehydrogenase, mitochondrial
Names
dimethylglycine dehydrogenase, mitochondrial
NP_037523.2

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012164.1 RefSeqGene

    Range
    4953..77063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_013391.3NP_037523.2  dimethylglycine dehydrogenase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_037523.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the supported protein.
    Source sequence(s)
    AA676742, AC008502, AF111858, AK057641, BP276968, CA397896
    Consensus CDS
    CCDS4044.1
    UniProtKB/TrEMBL
    B3KQ84
    UniProtKB/Swiss-Prot
    Q9UI17
    Related
    ENSP00000255189, OTTHUMP00000135299, ENST00000255189, OTTHUMT00000226963
    Conserved Domains (5) summary
    COG0404
    Location:464857
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:47435
    DadA; Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:531745
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:753845
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    cl21454
    Location:66419
    SDR; Short-chain dehydrogenases/reductases (SDR)

RNA

  1. NR_104002.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks three internal exons and contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008502, AF111858, AI302996, AK300894, BC022388, BP276968, BP425307
  2. NR_104003.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks five internal exons and contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008502, AI302996, AK303873, BC022388, BP276968, BP425307

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p2 Primary Assembly

    Range
    78997564..79069674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543354.1XP_011541656.1  

    Conserved Domains (4) summary
    COG0404
    Location:464751
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:47435
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:531745
    GCV_T; Aminomethyltransferase folate-binding domain
    cl21454
    Location:66419
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  2. XM_006714597.1XP_006714660.1  

    Conserved Domains (4) summary
    COG0404
    Location:464751
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:47435
    DadA; Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:531745
    GCV_T; Aminomethyltransferase folate-binding domain
    cl21454
    Location:66419
    SDR; Short-chain dehydrogenases/reductases (SDR)
  3. XM_011543355.1XP_011541657.1  

    Conserved Domains (4) summary
    COG0404
    Location:464750
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:47435
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:531745
    GCV_T; Aminomethyltransferase folate-binding domain
    cl21454
    Location:66419
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 Alternate CHM1_1.1

    Range
    77725882..77797969
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)