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Aliases for D2HGDH Gene

Aliases for D2HGDH Gene

  • D-2-Hydroxyglutarate Dehydrogenase 2 3 5
  • D2HGD 3 4
  • D-2-Hydroxyglutarate Dehydrogenase, Mitochondrial 3
  • EC 1.1.99.- 4
  • EC 1.1.99 61

External Ids for D2HGDH Gene

Previous GeneCards Identifiers for D2HGDH Gene

  • GC02P9M0151
  • GC02P242323
  • GC02P242673
  • GC02P234429

Summaries for D2HGDH Gene

Entrez Gene Summary for D2HGDH Gene

  • 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]

GeneCards Summary for D2HGDH Gene

D2HGDH (D-2-Hydroxyglutarate Dehydrogenase) is a Protein Coding gene. Diseases associated with D2HGDH include D-2-Hydroxyglutaric Aciduria and 2-Hydroxyglutaric Aciduria. Among its related pathways are Metabolism and Pyruvate metabolism and Citric Acid (TCA) cycle. GO annotations related to this gene include oxidoreductase activity and oxidoreductase activity, acting on CH-OH group of donors.

UniProtKB/Swiss-Prot for D2HGDH Gene

  • Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate.

Gene Wiki entry for D2HGDH Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for D2HGDH Gene

Genomics for D2HGDH Gene

Regulatory Elements for D2HGDH Gene

Enhancers for D2HGDH Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F241764 0.6 FANTOM5 Ensembl 38.7 +30.0 29980 0.5 RAD51 MAX RAD21 ZBTB7A D2HGDH ATG4B PIR37451 LOC105373976
GH02F241762 1.1 FANTOM5 Ensembl ENCODE 37.7 +28.7 28688 2.1 KLF1 PKNOX1 MAX EBF1 ZNF316 GATA3 POLR2A EED ZNF207 RCOR1 D2HGDH GAL3ST2 ENSG00000224272 ATG4B PDCD1 PIR37451 LOC105373976
GH02F241769 1.4 FANTOM5 Ensembl ENCODE 37.7 +38.2 38243 6.3 HDGF PKNOX1 MLX ZFP64 ARID4B DMAP1 YY1 SLC30A9 PAF1 SP5 D2HGDH GAL3ST2 ENSG00000223374 NEU4 LOC105373976 GC02P241774
GH02F241739 1.4 FANTOM5 Ensembl ENCODE 33.6 +6.0 6022 2.0 GATA3 NR2F1 RARA NFE2L2 D2HGDH NEU4 ENSG00000215023 ING5 GAL3ST2 RTP5 ATG4B ENSG00000215692 GC02P241747
GH02F241788 0.3 FANTOM5 20.9 +54.2 54211 0.4 CTCF PKNOX1 MTA2 CBFB JUNB EBF1 TBX21 RAD21 RELA EED D2HGDH ENSG00000224272 NEU4 ENSG00000234793 RTP5 ATG4B ENSG00000215023 GAL3ST2
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around D2HGDH on UCSC Golden Path with GeneCards custom track

Promoters for D2HGDH Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000610969 421 2001 HDGF MLX ARID4B SIN3A FEZF1 DMAP1 ZNF48 ZNF121 GLIS2 SP5

Genomic Location for D2HGDH Gene

Chromosome:
2
Start:
241,734,579 bp from pter
End:
241,768,816 bp from pter
Size:
34,238 bases
Orientation:
Plus strand

Genomic View for D2HGDH Gene

Genes around D2HGDH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
D2HGDH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for D2HGDH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for D2HGDH Gene

Proteins for D2HGDH Gene

  • Protein details for D2HGDH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N465-D2HDH_HUMAN
    Recommended name:
    D-2-hydroxyglutarate dehydrogenase, mitochondrial
    Protein Accession:
    Q8N465
    Secondary Accessions:
    • B4E3L6
    • E7ENP2
    • Q6IQ24
    • Q8N5Q8

    Protein attributes for D2HGDH Gene

    Size:
    521 amino acids
    Molecular mass:
    56416 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAX82020.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for D2HGDH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for D2HGDH Gene

Selected DME Specific Peptides for D2HGDH Gene

Q8N465:
  • CQAGCVLE
  • LDPKGILNPYK
  • AKHVVGYGHLGDGNLHLNVT

Post-translational modifications for D2HGDH Gene

  • Ubiquitination at Lys 64
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for D2HGDH
  • Cloud-Clone Corp. Antibodies for D2HGDH
  • Santa Cruz Biotechnology (SCBT) Antibodies for D2HGDH

Domains & Families for D2HGDH Gene

Graphical View of Domain Structure for InterPro Entry

Q8N465

UniProtKB/Swiss-Prot:

D2HDH_HUMAN :
  • Contains 1 FAD-binding PCMH-type domain.
  • Belongs to the FAD-binding oxidoreductase/transferase type 4 family.
Domain:
  • Contains 1 FAD-binding PCMH-type domain.
Family:
  • Belongs to the FAD-binding oxidoreductase/transferase type 4 family.
genes like me logo Genes that share domains with D2HGDH: view

No data available for Gene Families for D2HGDH Gene

Function for D2HGDH Gene

Molecular function for D2HGDH Gene

UniProtKB/Swiss-Prot CatalyticActivity:
(R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by zinc and cobalt.
UniProtKB/Swiss-Prot Function:
Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate.

Enzyme Numbers (IUBMB) for D2HGDH Gene

Gene Ontology (GO) - Molecular Function for D2HGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004458 D-lactate dehydrogenase (cytochrome) activity IBA --
GO:0016491 oxidoreductase activity IEA --
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors IEA --
GO:0050660 flavin adenine dinucleotide binding IEA --
GO:0051990 (R)-2-hydroxyglutarate dehydrogenase activity EXP,ISS 15070399
genes like me logo Genes that share ontologies with D2HGDH: view
genes like me logo Genes that share phenotypes with D2HGDH: view

Human Phenotype Ontology for D2HGDH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for D2HGDH

miRNA for D2HGDH Gene

miRTarBase miRNAs that target D2HGDH

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for D2HGDH Gene

Localization for D2HGDH Gene

Subcellular locations from UniProtKB/Swiss-Prot for D2HGDH Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for D2HGDH Gene COMPARTMENTS Subcellular localization image for D2HGDH gene
Compartment Confidence
mitochondrion 5
cytosol 2
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for D2HGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion ISS 15070399
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with D2HGDH: view

Pathways & Interactions for D2HGDH Gene

genes like me logo Genes that share pathways with D2HGDH: view

Gene Ontology (GO) - Biological Process for D2HGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006103 2-oxoglutarate metabolic process TAS --
GO:0010042 response to manganese ion ISS 15070399
GO:0010043 response to zinc ion ISS 15070399
GO:0019516 lactate oxidation IBA --
GO:0022904 respiratory electron transport chain IBA --
genes like me logo Genes that share ontologies with D2HGDH: view

No data available for SIGNOR curated interactions for D2HGDH Gene

Drugs & Compounds for D2HGDH Gene

(2) Drugs for D2HGDH Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0
Cobalt Pharma 165

(3) Additional Compounds for D2HGDH Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-hydroxyglutarate
D-2-Hydroxyglutaric acid
  • (R)-2-hydroxy-Pentanedioate
  • (R)-2-hydroxy-Pentanedioic acid
  • (R)-2-Hydroxyglutarate
  • (R)-2-Hydroxyglutaric acid
  • (R)-a-Hydroxyglutarate
2889-31-8
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with D2HGDH: view

Transcripts for D2HGDH Gene

mRNA/cDNA for D2HGDH Gene

(32) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(16) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for D2HGDH Gene

D-2-hydroxyglutarate dehydrogenase:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for D2HGDH Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c
SP1: - - -
SP2: - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - - -
SP6:
SP7: - -
SP8:

Relevant External Links for D2HGDH Gene

GeneLoc Exon Structure for
D2HGDH
ECgene alternative splicing isoforms for
D2HGDH

Expression for D2HGDH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for D2HGDH Gene

Protein differential expression in normal tissues from HIPED for D2HGDH Gene

This gene is overexpressed in Cervix (19.7), Liver (14.1), and Frontal cortex (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for D2HGDH Gene



NURSA nuclear receptor signaling pathways regulating expression of D2HGDH Gene:

D2HGDH

SOURCE GeneReport for Unigene cluster for D2HGDH Gene:

Hs.516813
genes like me logo Genes that share expression patterns with D2HGDH: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for D2HGDH Gene

Orthologs for D2HGDH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for D2HGDH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia D2HGDH 34 35
  • 98.13 (n)
dog
(Canis familiaris)
Mammalia D2HGDH 34 35
  • 85.07 (n)
cow
(Bos Taurus)
Mammalia D2HGDH 34 35
  • 81.76 (n)
mouse
(Mus musculus)
Mammalia D2hgdh 34 16 35
  • 79.66 (n)
rat
(Rattus norvegicus)
Mammalia D2hgdh 34
  • 79.49 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia D2HGDH 35
  • 76 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia D2HGDH 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves D2HGDH 34 35
  • 70.33 (n)
lizard
(Anolis carolinensis)
Reptilia D2HGDH 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia d2hgdh 34
  • 63.67 (n)
zebrafish
(Danio rerio)
Actinopterygii d2hgdh 34 35
  • 66.09 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004195 34
  • 59.3 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3835 34 35
  • 58.53 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_F54D5.12 34
  • 48.95 (n)
F54D5.12 35
  • 44 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL021C 34
  • 58.69 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F05753g 34
  • 54.26 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DLD2 34 35 37
  • 54.14 (n)
DLD3 35
  • 46 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G36400 34
  • 53.88 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06441 34
  • 58.32 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 58 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC713.03 34
  • 49.32 (n)
Species where no ortholog for D2HGDH was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for D2HGDH Gene

ENSEMBL:
Gene Tree for D2HGDH (if available)
TreeFam:
Gene Tree for D2HGDH (if available)

Paralogs for D2HGDH Gene

genes like me logo Genes that share paralogs with D2HGDH: view

No data available for Paralogs for D2HGDH Gene

Variants for D2HGDH Gene

Sequence variations from dbSNP and Humsavar for D2HGDH Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs121434360 D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721], Pathogenic 241,767,734(+) CAATG(C/T)GACGG nc-transcript-variant, reference, missense, utr-variant-3-prime, stop-lost
rs121434361 D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721], Pathogenic 241,742,524(+) GATCA(G/T)CCTCT nc-transcript-variant, reference, missense, utr-variant-5-prime
rs121434362 D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721], Pathogenic 241,767,718(+) ATGGT(A/G)ACCTG nc-transcript-variant, reference, synonymous-codon, missense, utr-variant-3-prime
rs267606759 D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721], Pathogenic 241,751,371(+) CCACC(A/G/T)ACCAG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense, utr-variant-3-prime
rs587783517 Pathogenic 241,743,697(+) CATGC(C/T)GCTGG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for D2HGDH Gene

Variant ID Type Subtype PubMed ID
dgv165e55 CNV loss 17911159
dgv7395n54 CNV loss 21841781
esv1008074 CNV deletion 20482838
esv1249069 CNV insertion 17803354
esv23937 CNV gain 19812545
esv2656823 CNV deletion 23128226
esv2722020 CNV deletion 23290073
esv2722021 CNV deletion 23290073
esv2722022 CNV deletion 23290073
esv2722023 CNV deletion 23290073
esv2722024 CNV deletion 23290073
esv2722025 CNV deletion 23290073
esv3561319 CNV deletion 23714750
esv3594839 CNV loss 21293372
esv3893578 CNV loss 25118596
esv988977 CNV gain 20482838
nsv1002941 CNV gain 25217958
nsv1006733 CNV gain 25217958
nsv10230 CNV loss 18304495
nsv1072091 CNV deletion 25765185
nsv1136320 CNV deletion 24896259
nsv1143974 CNV deletion 24896259
nsv513026 CNV loss 21212237
nsv584975 CNV loss 21841781
nsv584976 CNV loss 21841781
nsv584977 CNV loss 21841781
nsv584978 CNV gain+loss 21841781
nsv584981 CNV loss 21841781
nsv955300 CNV deletion 24416366
nsv997984 CNV gain 25217958

Variation tolerance for D2HGDH Gene

Residual Variation Intolerance Score: 69.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.04; 92.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for D2HGDH Gene

Human Gene Mutation Database (HGMD)
D2HGDH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
D2HGDH

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for D2HGDH Gene

Disorders for D2HGDH Gene

MalaCards: The human disease database

(3) MalaCards diseases for D2HGDH Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
d-2-hydroxyglutaric aciduria
  • d-2-hga
2-hydroxyglutaric aciduria
  • combined d-2- and l-2-hydroxyglutaric aciduria
hypotonia
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

D2HDH_HUMAN
  • D-2-hydroxyglutaric aciduria 1 (D2HGA1) [MIM:600721]: A rare recessive neurometabolic disorder causing developmental delay, epilepsy, hypotonia, and dysmorphic features. Both a mild and a severe phenotype exist. The severe phenotype is homogeneous and is characterized by early infantile-onset epileptic encephalopathy and cardiomyopathy. The mild phenotype has a more variable clinical presentation. Diagnosis is based on the presence of an excess of D-2-hydroxyglutaric acid in the urine. {ECO:0000269 PubMed:15609246, ECO:0000269 PubMed:16037974, ECO:0000269 PubMed:16081310}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for D2HGDH

Human Genome Epidemiology (HuGE) Navigator
D2HGDH
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
D2HGDH
genes like me logo Genes that share disorders with D2HGDH: view

No data available for Genatlas for D2HGDH Gene

Publications for D2HGDH Gene

  1. Mutations in the D-2-hydroxyglutarate dehydrogenase gene cause D-2- hydroxyglutaric aciduria. (PMID: 15609246) Struys E.A. … Jakobs C. (Am. J. Hum. Genet. 2005) 2 3 4 64
  2. Identification of a dehydrogenase acting on D-2-hydroxyglutarate. (PMID: 15070399) Achouri Y. … van Schaftingen E. (Biochem. J. 2004) 2 3 4 64
  3. D-2-Hydroxyglutaric aciduria in three patients with proven SSADH deficiency: genetic coincidence or a related biochemical epiphenomenon? (PMID: 16442322) Struys E.A. … Jakobs C. (Mol. Genet. Metab. 2006) 3 4 64
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier L.W. … Wilson R.K. (Nature 2005) 3 4 64
  5. Mutations in phenotypically mild D-2-hydroxyglutaric aciduria. (PMID: 16037974) Struys E.A. … Jakobs C. (Ann. Neurol. 2005) 3 4 64

Products for D2HGDH Gene

Sources for D2HGDH Gene

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