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    D2HGDH D-2-hydroxyglutarate dehydrogenase [ Homo sapiens (human) ]

    Gene ID: 728294, updated on 17-Jun-2024

    Summary

    Official Symbol
    D2HGDHprovided by HGNC
    Official Full Name
    D-2-hydroxyglutarate dehydrogenaseprovided by HGNC
    Primary source
    HGNC:HGNC:28358
    See related
    Ensembl:ENSG00000180902 MIM:609186; AllianceGenome:HGNC:28358
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    D2HGD
    Summary
    This gene encodes D-2hydroxyglutarate dehydrogenase, a mitochondrial enzyme belonging to the FAD-binding oxidoreductase/transferase type 4 family. This enzyme, which is most active in liver and kidney but also active in heart and brain, converts D-2-hydroxyglutarate to 2-ketoglutarate. Mutations in this gene are present in D-2-hydroxyglutaric aciduria, a rare recessive neurometabolic disorder causing developmental delay, epilepsy, hypotonia, and dysmorphic features. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 9.9), kidney (RPKM 7.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See D2HGDH in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (241734630..241768811)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (242238652..242271341)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242674045..242708226)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12553 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:242626177-242626439 Neighboring gene deoxythymidylate kinase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242640872-242641704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242641943-242642572 Neighboring gene inhibitor of growth family member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12558 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17431 Neighboring gene MPRA-validated peak4107 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242703699-242704312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242710178-242711090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242714429-242715049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242716291-242716911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242716912-242717532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242717533-242718152 Neighboring gene galactose-3-O-sulfotransferase 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:242727152-242728351 Neighboring gene CEB1 minisatellite repeat instability region Neighboring gene uncharacterized LOC124905349 Neighboring gene neuraminidase 4

    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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ42195, MGC25181

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables (R)-2-hydroxyglutarate dehydrogenase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables (R)-2-hydroxyglutarate dehydrogenase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables (R)-2-hydroxyglutarate dehydrogenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables FAD binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in 2-oxoglutarate metabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in malate metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    NOT involved_in response to calcium ion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in response to cobalt ion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    NOT involved_in response to magnesium ion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in response to manganese ion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in response to zinc ion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
     
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 

    General protein information

    Preferred Names
    D-2-hydroxyglutarate dehydrogenase, mitochondrial
    NP_001274178.1
    NP_001339753.1
    NP_689996.4
    XP_011510040.1
    XP_011510041.1
    XP_011510042.1
    XP_011510043.1
    XP_011510045.1
    XP_011510048.1
    XP_011510049.1
    XP_011510052.1
    XP_011510054.1
    XP_011510058.1
    XP_011510059.1
    XP_011510060.1
    XP_011510061.1
    XP_011510062.1
    XP_016860316.1
    XP_016860318.1
    XP_016860319.1
    XP_047301643.1
    XP_047301648.1
    XP_047301649.1
    XP_047301650.1
    XP_047301652.1
    XP_047301664.1
    XP_047301666.1
    XP_047301668.1
    XP_047301673.1
    XP_047301674.1
    XP_047301675.1
    XP_047301676.1
    XP_054199651.1
    XP_054199652.1
    XP_054199653.1
    XP_054199654.1
    XP_054199655.1
    XP_054199656.1
    XP_054199657.1
    XP_054199658.1
    XP_054199659.1
    XP_054199660.1
    XP_054199661.1
    XP_054199662.1
    XP_054199663.1
    XP_054199664.1
    XP_054199665.1
    XP_054199666.1
    XP_054199667.1
    XP_054199668.1
    XP_054199669.1
    XP_054199670.1
    XP_054199671.1
    XP_054199672.1
    XP_054199673.1
    XP_054199674.1
    XP_054199675.1
    XP_054199676.1
    XP_054199677.1
    XP_054199678.1
    XP_054199679.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_012012.1 RefSeqGene

      Range
      5016..39197
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001287249.2NP_001274178.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK094149, AK304764, AK304773, BC031817, BC036604, BC073980
      Consensus CDS
      CCDS74684.1
      UniProtKB/TrEMBL
      B3KSR6, B5MCV2
      Related
      ENSP00000384723.1, ENST00000403782.5
      Conserved Domains (1) summary
      COG0277
      Location:2386
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    2. NM_001352824.2NP_001339753.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC114730
      UniProtKB/TrEMBL
      B3KSR6
      Conserved Domains (1) summary
      COG0277
      Location:2333
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    3. NM_152783.5NP_689996.4  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_689996.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AK304764, AK304773, BC031817, BC036604, BC071598
      Consensus CDS
      CCDS33426.1
      UniProtKB/Swiss-Prot
      B4E3L6, E7ENP2, Q6IQ24, Q8N465, Q8N5Q8
      Related
      ENSP00000315351.4, ENST00000321264.9
      Conserved Domains (3) summary
      COG0277
      Location:69520
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:275515
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain

    RNA

    1. NR_109778.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK091725, AK304764, AK304773, BC031817, BC073980
      Related
      ENST00000400769.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      241734630..241768811
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011511750.4XP_011510052.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X13

      Conserved Domains (3) summary
      COG0277
      Location:69408
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:311408
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain
    2. XM_047445718.1XP_047301674.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X15

    3. XM_011511756.3XP_011510058.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X18

      Conserved Domains (1) summary
      COG0277
      Location:69370
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    4. XM_047445694.1XP_047301650.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    5. XM_011511743.3XP_011510045.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

      See identical proteins and their annotated locations for XP_011510045.1

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    6. XM_047445696.1XP_047301652.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    7. XM_047445710.1XP_047301666.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X11

    8. XM_017004830.3XP_016860319.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X10

    9. XM_017004829.3XP_016860318.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    10. XM_047445712.1XP_047301668.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X12

    11. XM_047445708.1XP_047301664.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X7

    12. XM_011511757.4XP_011510059.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X19

      UniProtKB/TrEMBL
      B4E3K7
      Conserved Domains (3) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
      pfam02913
      Location:311356
      FAD-oxidase_C; FAD linked oxidases, C-terminal domain
    13. XM_047445693.1XP_047301649.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X4

    14. XM_047445719.1XP_047301675.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X17

    15. XM_011511738.4XP_011510040.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011510040.1

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    16. XM_011511759.4XP_011510061.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      See identical proteins and their annotated locations for XP_011510061.1

      UniProtKB/TrEMBL
      B4E3K7
      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    17. XM_011511740.4XP_011510042.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011510042.1

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    18. XM_047445692.1XP_047301648.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X2

    19. XM_047445717.1XP_047301673.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X14

    20. XM_047445687.1XP_047301643.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    21. XM_011511739.3XP_011510041.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011510041.1

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    22. XM_017004827.3XP_016860316.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X3

    23. XM_011511741.4XP_011510043.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X5

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    24. XM_011511752.3XP_011510054.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X16

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    25. XM_011511747.4XP_011510049.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X9

      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    26. XM_047445720.1XP_047301676.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      UniProtKB/TrEMBL
      B4E3K7
    27. XM_011511760.4XP_011510062.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X21

      See identical proteins and their annotated locations for XP_011510062.1

      UniProtKB/TrEMBL
      B4E3K7
      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    28. XM_011511758.4XP_011510060.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      See identical proteins and their annotated locations for XP_011510060.1

      UniProtKB/TrEMBL
      B4E3K7
      Conserved Domains (2) summary
      COG0277
      Location:69286
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain
    29. XM_011511746.4XP_011510048.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X8

      Conserved Domains (2) summary
      COG0277
      Location:69339
      GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
      pfam01565
      Location:101238
      FAD_binding_4; FAD binding domain

    RNA

    1. XR_007081557.1 RNA Sequence

    2. XR_007081578.1 RNA Sequence

    3. XR_923016.4 RNA Sequence

    4. XR_923015.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      242238652..242271341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343694.1XP_054199669.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X13

    2. XM_054343696.1XP_054199671.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X15

    3. XM_054343699.1XP_054199674.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X18

    4. XM_054343684.1XP_054199659.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    5. XM_054343686.1XP_054199661.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    6. XM_054343685.1XP_054199660.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    7. XM_054343692.1XP_054199667.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X11

    8. XM_054343691.1XP_054199666.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X10

    9. XM_054343687.1XP_054199662.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    10. XM_054343693.1XP_054199668.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X12

    11. XM_054343688.1XP_054199663.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X7

    12. XM_054343700.1XP_054199675.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X19

      UniProtKB/TrEMBL
      B4E3K7
    13. XM_054343682.1XP_054199657.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X4

    14. XM_054343698.1XP_054199673.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X17

    15. XM_054343677.1XP_054199652.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    16. XM_054343703.1XP_054199678.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      UniProtKB/TrEMBL
      B4E3K7
    17. XM_054343679.1XP_054199654.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    18. XM_054343680.1XP_054199655.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X2

    19. XM_054343695.1XP_054199670.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X14

    20. XM_054343676.1XP_054199651.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    21. XM_054343678.1XP_054199653.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    22. XM_054343681.1XP_054199656.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X3

    23. XM_054343683.1XP_054199658.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X5

    24. XM_054343697.1XP_054199672.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X16

    25. XM_054343690.1XP_054199665.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X9

    26. XM_054343701.1XP_054199676.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      UniProtKB/TrEMBL
      B4E3K7
    27. XM_054343704.1XP_054199679.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X21

      UniProtKB/TrEMBL
      B4E3K7
    28. XM_054343702.1XP_054199677.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

      UniProtKB/TrEMBL
      B4E3K7
    29. XM_054343689.1XP_054199664.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X8

    RNA

    1. XR_008486500.1 RNA Sequence

    2. XR_008486501.1 RNA Sequence

    3. XR_008486503.1 RNA Sequence

    4. XR_008486502.1 RNA Sequence