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Aliases for IDH3A Gene

Aliases for IDH3A Gene

  • Isocitrate Dehydrogenase 3 (NAD(+)) Alpha 2 3 5
  • EC 4 61
  • Isocitrate Dehydrogenase [NAD] Subunit Alpha, Mitochondrial 2
  • NAD(H)-Specific Isocitrate Dehydrogenase Alpha Subunit 2
  • Isocitrate Dehydrogenase (NAD+) Alpha Chain 2
  • Isocitrate Dehydrogenase 3 (NAD+) Alpha 2
  • Isocitric Dehydrogenase Subunit Alpha 4
  • NAD(+)-Specific ICDH Subunit Alpha 4
  • Isocitric Dehydrogenase 2
  • NAD+-Specific ICDH 2
  • H-IDH Alpha 2
  • EC 1.1.1 61

External Ids for IDH3A Gene

Previous GeneCards Identifiers for IDH3A Gene

  • GC15P074520
  • GC15P071531
  • GC15P076017
  • GC15P076157
  • GC15P076228
  • GC15P078441
  • GC15P055199
  • GC15P078423

Summaries for IDH3A Gene

Entrez Gene Summary for IDH3A Gene

  • Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the alpha subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. [provided by RefSeq, Jul 2008]

GeneCards Summary for IDH3A Gene

IDH3A (Isocitrate Dehydrogenase 3 (NAD(+)) Alpha) is a Protein Coding gene. Among its related pathways are Citrate cycle (TCA cycle) and Pyruvate metabolism and Citric Acid (TCA) cycle. GO annotations related to this gene include magnesium ion binding and oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor.

Gene Wiki entry for IDH3A Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IDH3A Gene

Genomics for IDH3A Gene

Regulatory Elements for IDH3A Gene

Enhancers for IDH3A 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
GH15G078146 1.4 ENCODE dbSUPER 17.6 +17.1 17138 5.2 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF207 FOS IDH3A SH2D7 TBC1D2B ENSG00000199633 CIB2 WDR61 ENSG00000260988 GC15P078155
GH15G078166 1.4 Ensembl ENCODE dbSUPER 17.5 +39.2 39218 8.6 TBP PKNOX1 TBL1XR1 ZBTB40 ZNF766 CBX5 RELB IKZF2 CREM JUNB CIB2 IDH3A TBC1D2B SH2D7 ENSG00000199633 GC15P078155 PIR56006
GH15G078156 0.8 dbSUPER 15.4 +25.7 25663 1.5 HDAC1 FEZF1 YY1 SCRT2 CEBPB OVOL3 TSHZ1 ZNF843 NR2F2 MAFF CIB2 IDH3A ENSG00000199633 SH2D7 TBC1D2B GC15P078155 PIR56006
GH15G078087 1.6 FANTOM5 Ensembl ENCODE dbSUPER 7.7 -43.2 -43239 1.5 SOX13 FOXA2 RELA ZNF7 YY1 ZNF507 FOSL1 EED HNF4G NFE2 LOC645752 IDH3A DNAJA4 IREB2 ENSG00000199633 GC15M078092 SH2D7
GH15G078081 1.8 FANTOM5 Ensembl ENCODE dbSUPER 5.6 -48.4 -48398 3.0 ATF1 FOXA2 SIN3A DMAP1 YY1 GLIS2 FOS SREBF1 RCOR2 KDM1A LOC645752 TBC1D2B IDH3A DNAJA4 IREB2 SH2D7 GC15M078092 ENSG00000199633
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around IDH3A on UCSC Golden Path with GeneCards custom track

Promoters for IDH3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for IDH3A Gene

78,131,498 bp from pter
78,171,949 bp from pter
40,452 bases
Plus strand

Genomic View for IDH3A Gene

Genes around IDH3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IDH3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IDH3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IDH3A Gene

Proteins for IDH3A Gene

  • Protein details for IDH3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • D3DW83
    • Q9H3X0

    Protein attributes for IDH3A Gene

    366 amino acids
    Molecular mass:
    39592 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1.

    Three dimensional structures from OCA and Proteopedia for IDH3A Gene

    Alternative splice isoforms for IDH3A Gene


neXtProt entry for IDH3A Gene

Selected DME Specific Peptides for IDH3A Gene


Post-translational modifications for IDH3A Gene

  • Ubiquitination at posLast=5858, posLast=7777, and isoforms=2100
  • Modification sites at PhosphoSitePlus

Domains & Families for IDH3A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the isocitrate and isopropylmalate dehydrogenases family.
  • Belongs to the isocitrate and isopropylmalate dehydrogenases family.
genes like me logo Genes that share domains with IDH3A: view

No data available for Gene Families for IDH3A Gene

Function for IDH3A Gene

Molecular function for IDH3A Gene

GENATLAS Biochemistry:
isocitrate dehydrogenase 3,alpha subunit,NADH dependent,mitochondrial matrix,catalyzing the third step of citric acid cycle
UniProtKB/Swiss-Prot CatalyticActivity:
Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH.

Enzyme Numbers (IUBMB) for IDH3A Gene

Gene Ontology (GO) - Molecular Function for IDH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IEA --
GO:0004449 isocitrate dehydrogenase (NAD+) activity IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with IDH3A: view
genes like me logo Genes that share phenotypes with IDH3A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for IDH3A Gene

Localization for IDH3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for IDH3A Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IDH3A gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for IDH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix TAS --
GO:0043209 myelin sheath IEA --
genes like me logo Genes that share ontologies with IDH3A: view

Pathways & Interactions for IDH3A Gene

genes like me logo Genes that share pathways with IDH3A: view

Gene Ontology (GO) - Biological Process for IDH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process NAS 8833160
GO:0006099 tricarboxylic acid cycle TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with IDH3A: view

No data available for SIGNOR curated interactions for IDH3A Gene

Drugs & Compounds for IDH3A Gene

(6) Drugs for IDH3A Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Carbon dioxide Approved, Vet_approved Pharma 0
Manganese Approved Nutra 34
Isocitric acid Experimental Pharma 0
NADH Nutra Target 0
NAD Pharma Full agonist, Agonist 0

(2) Additional Compounds for IDH3A Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
genes like me logo Genes that share compounds with IDH3A: view

Transcripts for IDH3A Gene

Unigene Clusters for IDH3A Gene

Isocitrate dehydrogenase 3 (NAD+) alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IDH3A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c ^ 11a · 11b · 11c ^ 12a · 12b · 12c · 12d · 12e ^
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - -
SP4: - - - - - - -
SP5: - - - - - - -
SP6: - - - - -
SP7: - - - - -
SP8: - - - - - - - - -
SP9: - - - - -
SP10: - - - -
SP11: - - - - - - -
SP12: - - - - - - -
SP14: - - - -
SP15: - - - - -
SP16: - - - - - - - -
SP17: - - - - - -
SP18: - - -
SP19: - - -

ExUns: 13 ^ 14 ^ 15a · 15b ^ 16a · 16b

Relevant External Links for IDH3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for IDH3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IDH3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IDH3A Gene

This gene is overexpressed in Heart - Left Ventricle (x4.1).

Protein differential expression in normal tissues from HIPED for IDH3A Gene

This gene is overexpressed in Brain (8.6) and Nasal epithelium (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for IDH3A Gene

Protein tissue co-expression partners for IDH3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of IDH3A Gene:


SOURCE GeneReport for Unigene cluster for IDH3A Gene:


Evidence on tissue expression from TISSUES for IDH3A Gene

  • Nervous system(5)
  • Heart(4.5)
  • Muscle(2.7)
  • Intestine(2.4)
  • Kidney(2.2)
genes like me logo Genes that share expression patterns with IDH3A: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IDH3A Gene

Orthologs for IDH3A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for IDH3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia IDH3A 34 35
  • 99.64 (n)
(Monodelphis domestica)
Mammalia IDH3A 35
  • 95 (a)
(Ornithorhynchus anatinus)
Mammalia IDH3A 35
  • 94 (a)
(Bos Taurus)
Mammalia IDH3A 34 35
  • 92.53 (n)
(Canis familiaris)
Mammalia IDH3A 34 35
  • 91.07 (n)
(Mus musculus)
Mammalia Idh3a 34 16 35
  • 89.34 (n)
(Rattus norvegicus)
Mammalia Idh3a 34
  • 88.98 (n)
(Gallus gallus)
Aves IDH3A 34 35
  • 80.9 (n)
(Anolis carolinensis)
Reptilia IDH3A 35
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia idh3a 34
  • 76.5 (n)
MGC76128 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.15952 34
(Danio rerio)
Actinopterygii idh3a 34 35
  • 75.78 (n)
zgc56380 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9912 34
fruit fly
(Drosophila melanogaster)
Insecta CG12233 36
  • 71 (a)
l(1)G0156 34 35
  • 64.6 (n)
CG3483 36 35
  • 39 (a)
CG32026 35
  • 30 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002728 34
  • 63.81 (n)
(Caenorhabditis elegans)
Secernentea F43G9.1 36
  • 65 (a)
idha-1 34 35
  • 63.57 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E03125g 34
  • 55.59 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IDH2 34 35 37
  • 54.48 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR137C 34
  • 53.92 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons IDH-V 34
  • 58.24 (n)
(Glycine max)
eudicotyledons Gma.7251 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6781 34
(Oryza sativa)
Liliopsida Os01g0276100 34
  • 58.91 (n)
Os.207 34
(Hordeum vulgare)
Liliopsida Hv.620 34
(Triticum aestivum)
Liliopsida Ta.24979 34
(Zea mays)
Liliopsida Zm.3035 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 73 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU07697 34
  • 58.28 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes idh2 34
  • 58.23 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8758 34
Species where no ortholog for IDH3A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for IDH3A Gene

Gene Tree for IDH3A (if available)
Gene Tree for IDH3A (if available)

Paralogs for IDH3A Gene

No data available for Paralogs for IDH3A Gene

Variants for IDH3A Gene

Sequence variations from dbSNP and Humsavar for IDH3A Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1000028333 -- 78,164,828(+) ATGCT(C/G/T)GAGGC intron-variant
rs1000370566 -- 78,158,216(+) GAATG(A/G)AATGT intron-variant
rs1000667107 -- 78,157,887(+) TGAAC(G/T)CTGGG intron-variant
rs1000996110 -- 78,157,457(+) CATCT(C/G)ATAAA intron-variant
rs1001039260 -- 78,162,639(+) CTCCC(A/G)GGTTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for IDH3A Gene

Variant ID Type Subtype PubMed ID
nsv1116464 OTHER inversion 24896259

Variation tolerance for IDH3A Gene

Residual Variation Intolerance Score: 38.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.10; 22.44% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for IDH3A Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IDH3A Gene

Disorders for IDH3A Gene

Relevant External Links for IDH3A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for IDH3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for IDH3A Gene

Publications for IDH3A Gene

  1. Assignment of the human mitochondrial NAD+ -specific isocitrate dehydrogenase alpha subunit (IDH3A) gene to 15q25.1-->q25.2by in situ hybridization. (PMID: 8833160) Huh T.L. … Inazawa J. (Genomics 1996) 2 3 22 64
  2. Characterization of a cDNA clone for human NAD(+)-specific isocitrate dehydrogenase alpha-subunit and structural comparison with its isoenzymes from different species. (PMID: 7755589) Kim Y.O. … Huh T.L. (Biochem. J. 1995) 3 4 22 64
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells. (PMID: 27637333) Gabriel C.H. … Baumgrass R. (J. Biol. Chem. 2016) 3 64

Products for IDH3A Gene

Sources for IDH3A Gene

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