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

Gene ID: 728294, updated on 3-Apr-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
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Genomic context

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

  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

  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

  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

  27. XM_054343704.1XP_054199679.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X21

  28. XM_054343702.1XP_054199677.1  D-2-hydroxyglutarate dehydrogenase, mitochondrial isoform X20

  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