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    DMGDH dimethylglycine dehydrogenase [ Homo sapiens (human) ]

    Gene ID: 29958, updated on 3-Nov-2024

    Summary

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    Official Symbol
    DMGDHprovided by HGNC
    Official Full Name
    dimethylglycine dehydrogenaseprovided by HGNC
    Primary source
    HGNC:HGNC:24475
    See related
    Ensembl:ENSG00000132837 MIM:605849; AllianceGenome:HGNC:24475
    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
    mouse all
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    Genomic context

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    See DMGDH in Genome Data Viewer
    Location:
    5q14.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (78997564..79069674, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79478676..79550778, complement)
    RS_2024_09 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 uncharacterized LOC124900191 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:77995230-77996429 Neighboring gene Sharpr-MPRA regulatory region 2428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:78105507-78106007 Neighboring gene arylsulfatase B Neighboring gene Sharpr-MPRA regulatory region 14877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270456-78270975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270976-78271494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16127 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:78293710-78294909 Neighboring gene IMPACT pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr5:78317526-78318027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:78407958-78408802 Neighboring gene uncharacterized LOC124901012 Neighboring gene betaine--homocysteine S-methyltransferase 2 Neighboring gene betaine--homocysteine S-methyltransferase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Molecular basis of dimethylglycine dehydrogenase deficiency associated with pathogenic variant H109R. McAndrew RP, et al. J Inherit Metab Dis, 2008 Dec. PMID 18937046, Free PMC Article
    2. Structure and analysis of the human dimethylglycine dehydrogenase gene. Binzak BA, et al. Mol Genet Metab, 2000 Mar. PMID 10767172
    3. Dimethylglycine Deficiency and the Development of Diabetes. Magnusson M, et al. Diabetes, 2015 Aug. PMID 25795213, Free PMC Article
    4. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. Augustin P, et al. FEBS J, 2016 Oct. PMID 27486859, Free PMC Article
    5. Nonalcoholic steatohepatitis is associated with a state of betaine-insufficiency. Sookoian S, et al. Liver Int, 2017 Apr. PMID 27614103

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our study suggested markers in BHMT/BHMT2 and DMGDH might affect the risk of NSCL/P through pairwise interaction.
      Title: Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft.
    2. In nonalcoholic fatty liver disease patient, the missense variant p.Ser646Pro (rs1805074) in DMGDH gene was significantly associated with disease severity and circulating levels of dimethylglycine.
      Title: Nonalcoholic steatohepatitis is associated with a state of betaine-insufficiency.
    3. The structure-based analysis provided new insights into the kinetic properties of dimethylglycine dehydrogenase in particular with respect to oxygen reactivity.
      Title: Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant.
    4. In agreement with previous studies, we show that the genetic variant rs921943 in DMGDH is significantly associated with selenium status in United Kingdom pregnant women.
      Title: Genetic polymorphisms that affect selenium status and response to selenium supplementation in United Kingdom pregnant women.
    5. Genetic variation of DMGDH was associated with higher plasma insulin, increased insulin resistance and increased risk of incident diabetes.
      Title: Dimethylglycine Deficiency and the Development of Diabetes.
    6. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    9. analysis of dimethylglycine dehydrogenase deficiency associated with pathogenic variant H109R
      Title: Molecular basis of dimethylglycine dehydrogenase deficiency associated with pathogenic variant H109R.
    10. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Oral facial clefts and gene polymorphisms in metabolism of folate/one-carbon and vitamin A: a pathway-wide association study.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

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

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
    EBI GWAS Catalog
    Genome-wide association study of selenium concentrations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

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

    General protein information

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    Preferred Names
    dimethylglycine dehydrogenase, mitochondrial
    NP_037523.2
    XP_006714660.1
    XP_011541657.1
    XP_054208450.1
    XP_054208451.1

    NCBI Reference Sequences (RefSeq)

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    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_013391.3 → NP_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
      B2RBN0, B4E1J9, Q9UI17
      UniProtKB/TrEMBL
      B3KQ84
      Related
      ENSP00000255189.3, ENST00000255189.8
      Conserved Domains (6) summary
      COG0404
      Location:464 → 857
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:47 → 435
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:482 → 745
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:753 → 845
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:417 → 472
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:44 → 90
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    RNA

    1. NR_104002.3 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, AC020937, AF111858, AI302996, AK300894, BC022388, BP276968, BP425307
      Related
      ENST00000523732.1

    2. NR_104003.3 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, AC020937, AI302996, AK303873, BC022388, BP276968, BP425307

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_011543355.3 → XP_011541657.1  dimethylglycine dehydrogenase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B3KQ84
      Conserved Domains (5) summary
      COG0404
      Location:464 → 750
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:47 → 435
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:482 → 745
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam16350
      Location:417 → 472
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:44 → 90
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    2. XM_006714597.3 → XP_006714660.1  dimethylglycine dehydrogenase, mitochondrial isoform X1

      UniProtKB/TrEMBL
      B3KQ84
      Conserved Domains (5) summary
      COG0404
      Location:464 → 751
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:47 → 435
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:482 → 745
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam16350
      Location:417 → 472
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:44 → 90
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      79478676..79550778 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352476.1 → XP_054208451.1  dimethylglycine dehydrogenase, mitochondrial isoform X2

    2. XM_054352475.1 → XP_054208450.1  dimethylglycine dehydrogenase, mitochondrial isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UI17.2 GenPept UniProtKB/Swiss-Prot:Q9UI17

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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