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DMGDH dimethylglycine dehydrogenase [ Homo sapiens (human) ]

Gene ID: 29958, updated on 12-Jul-2019

Summary

Official Symbol
DMGDHprovided by HGNC
Official Full Name
dimethylglycine dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:24475
See related
Ensembl:ENSG00000132837 MIM:605849
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]
Expression
Biased expression in kidney (RPKM 31.5), liver (RPKM 24.3) and 1 other tissue See more
Orthologs

Genomic context

See DMGDH in Genome Data Viewer
Location:
5q14.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 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 LHFPL tetraspan subfamily member 2 Neighboring gene Sharpr-MPRA regulatory region 2428 Neighboring gene arylsulfatase B Neighboring gene IMPACT pseudogene Neighboring gene betaine--homocysteine S-methyltransferase 2 Neighboring gene betaine--homocysteine S-methyltransferase

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

Pathways from BioSystems

  • Choline catabolism, organism-specific biosystem (from REACTOME)
    Choline catabolism, organism-specific biosystemCholine is an essential water-soluble nutrient in humans, serving as a precursor of phospholipids and the neurotransmitter acetylcholine. It is often associated with B vitamins based on its chemical ...
  • Glycerophospholipid biosynthesis, organism-specific biosystem (from REACTOME)
    Glycerophospholipid biosynthesis, organism-specific biosystemGlycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids...
  • 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
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
dimethylglycine dehydrogenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dimethylglycine dehydrogenase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
electron transfer activity NAS
Non-traceable Author Statement
more info
PubMed 
oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
amino-acid betaine catabolic process IEA
Inferred from Electronic Annotation
more info
 
choline catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
choline catabolic process TAS
Traceable Author Statement
more info
 
choline metabolic process NAS
Non-traceable Author Statement
more info
PubMed 
electron transport chain IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial matrix NAS
Non-traceable Author Statement
more info
PubMed 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
dimethylglycine dehydrogenase, mitochondrial
NP_037523.2
XP_006714660.1
XP_011541657.1

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q9UI17
    UniProtKB/TrEMBL
    B3KQ84
    Related
    ENSP00000255189.3, ENST00000255189.7
    Conserved Domains (6) summary
    COG0404
    Location:464857
    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:482745
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:753845
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:417472
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:4490
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

RNA

  1. NR_104002.2 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
    Related
    ENST00000523732.1
  2. NR_104003.2 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 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006714597.2XP_006714660.1  dimethylglycine dehydrogenase, mitochondrial isoform X1

    Conserved Domains (5) 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:482745
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam16350
    Location:417472
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:4490
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
  2. XM_011543355.2XP_011541657.1  dimethylglycine dehydrogenase, mitochondrial isoform X2

    Conserved Domains (5) 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:482745
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam16350
    Location:417472
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:4490
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins
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