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

Gene ID: 728294, updated on 21-Jan-2020

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
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

Genomic context

See D2HGDH in Genome Data Viewer
Location:
2q37.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (241734629..241768816)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242674030..242708231)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene deoxythymidylate kinase Neighboring gene inhibitor of growth family member 5 Neighboring gene uncharacterized LOC105373976 Neighboring gene galactose-3-O-sulfotransferase 2 Neighboring gene CEB1 minisatellite repeat instability region

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

Homology

Clone Names

  • FLJ42195, MGC25181

Gene Ontology Provided by GOA

Function Evidence Code Pubs
(R)-2-hydroxyglutarate dehydrogenase activity EXP
Inferred from Experiment
more info
PubMed 
(R)-2-hydroxyglutarate dehydrogenase activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
FAD binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
2-oxoglutarate metabolic process TAS
Traceable Author Statement
more info
 
cellular protein metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
NOT response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
response to cobalt ion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
NOT response to magnesium ion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
response to manganese ion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
response to zinc ion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
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
 
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_011510036.1
XP_011510037.1
XP_011510038.1
XP_011510039.1
XP_011510040.1
XP_011510041.1
XP_011510042.1
XP_011510043.1
XP_011510045.1
XP_011510046.1
XP_011510047.1
XP_011510048.1
XP_011510049.1
XP_011510051.1
XP_011510052.1
XP_011510053.1
XP_011510054.1
XP_011510055.1
XP_011510058.1
XP_011510059.1
XP_011510060.1
XP_011510061.1
XP_011510062.1
XP_016860316.1
XP_016860317.1
XP_016860318.1
XP_016860319.1
XP_016860321.1
XP_024308870.1
XP_024308871.1

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_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/Swiss-Prot
    Q8N465
    UniProtKB/TrEMBL
    B3KSR6, B4E3K7, B5MCV2
    Related
    ENSP00000384723.1, ENST00000403782.5
    Conserved Domains (3) summary
    TIGR00387
    Location:3381
    glcD; glycolate oxidase, subunit GlcD
    pfam01565
    Location:2104
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:141381
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  2. NM_001352824.2NP_001339753.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC114730
    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
    Q8N465
    UniProtKB/TrEMBL
    B4E3K7
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    241734629..241768816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511734.2XP_011510036.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X1

    Conserved Domains (3) summary
    COG0277
    Location:69560
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:311555
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  2. XM_011511735.2XP_011510037.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X2

    Conserved Domains (3) summary
    COG0277
    Location:69546
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:311541
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  3. XM_011511736.2XP_011510038.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X3

    Conserved Domains (3) summary
    COG0277
    Location:69534
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:275529
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  4. XM_011511756.2XP_011510058.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

    Conserved Domains (3) summary
    COG0277
    Location:69370
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:277364
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  5. XM_011511750.3XP_011510052.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X16

    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
  6. XM_011511744.2XP_011510046.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X10

    See identical proteins and their annotated locations for XP_011510046.1

    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
  7. XM_011511737.3XP_011510039.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X5

    Conserved Domains (3) summary
    COG0277
    Location:69466
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:311466
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  8. XM_017004828.2XP_016860317.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X8

  9. XM_011511749.3XP_011510051.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X15

    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_011511745.3XP_011510047.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X11

    Conserved Domains (3) summary
    COG0277
    Location:69402
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
    pfam01565
    Location:101238
    FAD_binding_4; FAD binding domain
    pfam02913
    Location:311405
    FAD-oxidase_C; FAD linked oxidases, C-terminal domain
  11. XM_011511753.3XP_011510055.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X19

    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
  12. XM_011511743.2XP_011510045.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X10

    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
  13. XM_011511751.2XP_011510053.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X17

    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
  14. XM_017004830.2XP_016860319.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X14

  15. XM_017004829.2XP_016860318.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X10

    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_011511757.3XP_011510059.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X21

    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
  17. XM_011511738.3XP_011510040.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    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
  18. XM_011511759.3XP_011510061.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X22

    See identical proteins and their annotated locations for XP_011510061.1

    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
  19. XM_017004827.2XP_016860316.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X7

  20. XM_011511741.3XP_011510043.1  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
  21. XM_011511747.3XP_011510049.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X13

    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_011511760.3XP_011510062.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X24

    See identical proteins and their annotated locations for XP_011510062.1

    UniProtKB/Swiss-Prot
    Q8N465
    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
  23. XM_024453103.1XP_024308871.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X23

    Conserved Domains (1) summary
    COG0277
    Location:69286
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]
  24. XM_011511740.3XP_011510042.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    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
  25. XM_011511739.2XP_011510041.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X6

    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
  26. XM_011511752.2XP_011510054.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X18

    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
  27. XM_011511758.3XP_011510060.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X22

    See identical proteins and their annotated locations for XP_011510060.1

    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
  28. XM_017004832.2XP_016860321.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X25

  29. XM_011511746.3XP_011510048.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X12

    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
  30. XM_024453102.1XP_024308870.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X4

    Conserved Domains (1) summary
    COG0277
    Location:22484
    GlcD; FAD/FMN-containing dehydrogenase [Energy production and conversion]

RNA

  1. XR_923004.3 RNA Sequence

  2. XR_923011.3 RNA Sequence

  3. XR_001738918.2 RNA Sequence

  4. XR_923007.3 RNA Sequence

  5. XR_001738919.2 RNA Sequence

  6. XR_923014.3 RNA Sequence

  7. XR_923005.2 RNA Sequence

  8. XR_923009.2 RNA Sequence

  9. XR_241434.4 RNA Sequence

  10. XR_002959334.1 RNA Sequence

  11. XR_923010.2 RNA Sequence

  12. XR_002959335.1 RNA Sequence

  13. XR_923012.2 RNA Sequence

  14. XR_923016.3 RNA Sequence

  15. XR_923013.2 RNA Sequence

  16. XR_923015.2 RNA Sequence

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