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Aliases for IDH3B Gene

Aliases for IDH3B Gene

  • Isocitrate Dehydrogenase 3 (NAD(+)) Beta 2 3
  • Isocitrate Dehydrogenase 3 (NAD+) Beta 2 3 5
  • Isocitric Dehydrogenase Subunit Beta 3 4
  • NAD(+)-Specific ICDH Subunit Beta 3 4
  • EC 4 63
  • EC 1.1.1 63
  • RP46 3

External Ids for IDH3B Gene

Previous GeneCards Identifiers for IDH3B Gene

  • GC20M002627
  • GC20M002634
  • GC20M002587
  • GC20M002639

Summaries for IDH3B Gene

Entrez Gene Summary for IDH3B 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 beta subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. Three alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for IDH3B Gene

IDH3B (Isocitrate Dehydrogenase 3 (NAD(+)) Beta) is a Protein Coding gene. Diseases associated with IDH3B include Retinitis Pigmentosa 46 and Idh3b-Related Retinitis Pigmentosa. Among its related pathways are Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. and Pyruvate metabolism and Citric Acid (TCA) cycle. GO annotations related to this gene include magnesium ion binding and NAD binding. An important paralog of this gene is IDH3G.

Gene Wiki entry for IDH3B Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IDH3B Gene

Genomics for IDH3B Gene

Regulatory Elements for IDH3B Gene

Enhancers for IDH3B Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around IDH3B on UCSC Golden Path with GeneCards custom track

Promoters for IDH3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around IDH3B on UCSC Golden Path with GeneCards custom track

Genomic Location for IDH3B Gene

2,658,394 bp from pter
2,664,219 bp from pter
5,826 bases
Minus strand

Genomic View for IDH3B Gene

Genes around IDH3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IDH3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IDH3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IDH3B Gene

Proteins for IDH3B Gene

  • Protein details for IDH3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B2RDR1
    • D3DVX2
    • D3DVX3
    • O95106
    • Q5JXS8
    • Q9NQ06
    • Q9NQ07
    • Q9NUZ0
    • Q9UEX0
    • Q9UG99

    Protein attributes for IDH3B Gene

    385 amino acids
    Molecular mass:
    42184 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.

    Alternative splice isoforms for IDH3B Gene


neXtProt entry for IDH3B Gene

Proteomics data for IDH3B Gene at MOPED

Post-translational modifications for IDH3B Gene

  • Ubiquitination at Lys 199
  • Modification sites at PhosphoSitePlus

Other Protein References for IDH3B Gene

Domains & Families for IDH3B Gene

Suggested Antigen Peptide Sequences for IDH3B Gene

GenScript: Design optimal peptide antigens:

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 IDH3B: view

No data available for Gene Families for IDH3B Gene

Function for IDH3B Gene

Molecular function for IDH3B Gene

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

Enzyme Numbers (IUBMB) for IDH3B Gene

genes like me logo Genes that share phenotypes with IDH3B: view

Human Phenotype Ontology for IDH3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for IDH3B Gene

Localization for IDH3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for IDH3B Gene


Subcellular locations from

Jensen Localization Image for IDH3B Gene COMPARTMENTS Subcellular localization image for IDH3B gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for IDH3B Gene

Pathways & Interactions for IDH3B Gene

genes like me logo Genes that share pathways with IDH3B: view

Gene Ontology (GO) - Biological Process for IDH3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006099 tricarboxylic acid cycle IEA,TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with IDH3B: view

No data available for SIGNOR curated interactions for IDH3B Gene

Drugs & Compounds for IDH3B Gene

(5) Drugs for IDH3B Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Isocitric acid Experimental Pharma 0
NADH Nutra Target 0
Manganese Pharma 32
NAD Pharma Full agonist, Agonist 0
Magnesium Nutra 0

(3) Additional Compounds for IDH3B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
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 IDH3B: view

Transcripts for IDH3B Gene

Unigene Clusters for IDH3B Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for IDH3B Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b ^ 11 ^ 12a · 12b ^
SP1: - - -
SP2: - - - - -
SP3: - -
SP4: - - - - -
SP5: - - - -
SP6: -
SP7: -
SP8: -
SP9: -
SP10: - - -
SP11: -
SP12: -
SP13: -

ExUns: 13a · 13b

Relevant External Links for IDH3B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for IDH3B Gene

mRNA expression in normal human tissues for IDH3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for IDH3B Gene

This gene is overexpressed in Brain (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for IDH3B Gene

SOURCE GeneReport for Unigene cluster for IDH3B Gene Hs.436405

genes like me logo Genes that share expression patterns with IDH3B: view

Protein tissue co-expression partners for IDH3B Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for IDH3B Gene

Orthologs for IDH3B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for IDH3B Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia IDH3B 35
  • 92.19 (n)
  • 94.27 (a)
IDH3B 36
  • 94 (a)
(Canis familiaris)
Mammalia IDH3B 35
  • 92.01 (n)
  • 96.35 (a)
-- 36
  • 96 (a)
-- 36
  • 74 (a)
(Mus musculus)
Mammalia Idh3b 35
  • 88.34 (n)
  • 92.43 (a)
Idh3b 16
Idh3b 36
  • 93 (a)
(Pan troglodytes)
Mammalia IDH3B 35
  • 99.83 (n)
  • 99.74 (a)
IDH3B 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Idh3B 35
  • 90.02 (n)
  • 94.27 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 91 (a)
-- 36
  • 74 (a)
(Gallus gallus)
Aves IDH3B 35
  • 78.51 (n)
  • 85 (a)
IDH3B 36
  • 75 (a)
(Anolis carolinensis)
Reptilia IDH3B 36
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia idh3b 35
  • 76.79 (n)
  • 86.14 (a)
Str.8848 35
(Danio rerio)
Actinopterygii Dr.12046 35
idh3b 35
  • 74.88 (n)
  • 86.05 (a)
idh3b 36
  • 77 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3483 37
  • 34 (a)
CG5028 37
  • 43 (a)
CG6439 37
  • 60 (a)
CG6439 35
  • 64.3 (n)
  • 64.81 (a)
CG6439 36
  • 57 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007786 35
  • 61.13 (n)
  • 63.2 (a)
(Caenorhabditis elegans)
Secernentea C37E2.1 37
  • 60 (a)
F35G12.2 37
  • 47 (a)
idhb-1 35
  • 60.55 (n)
  • 64.22 (a)
idhb-1 36
  • 56 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL223W 35
  • 56.16 (n)
  • 50.45 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04103g 35
  • 54.65 (n)
  • 51.21 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IDH1 35
  • 51.81 (n)
  • 48.19 (a)
IDH1 36
  • 45 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons IDH2 35
  • 56.91 (n)
  • 52.96 (a)
(Oryza sativa)
Liliopsida Os04g0479200 35
  • 55.04 (n)
  • 51.71 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00775 35
  • 55.59 (n)
  • 50.6 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes idh1 35
  • 52.69 (n)
  • 48.68 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7868 36
  • 61 (a)
Species with no ortholog for IDH3B:
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 IDH3B Gene

Gene Tree for IDH3B (if available)
Gene Tree for IDH3B (if available)

Paralogs for IDH3B Gene

Paralogs for IDH3B Gene

(2) SIMAP similar genes for IDH3B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with IDH3B: view

Variants for IDH3B Gene

Sequence variations from dbSNP and Humsavar for IDH3B Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs3178817 - 2,664,181(-) GGCGG(C/T)ATTGA nc-transcript-variant, reference, missense
rs11542741 - 2,660,730(-) GAGCA(G/T)ACAGA nc-transcript-variant, reference, missense
VAR_054851 Retinitis pigmentosa 46 (RP46)
VAR_056005 -
rs2235954 -- 2,664,329(-) GCAAG(A/G)AAAAG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for IDH3B Gene

Variant ID Type Subtype PubMed ID
nsv470535 CNV Gain 18288195
nsv458852 CNV Loss 19166990
esv988063 CNV Insertion 20482838
esv1188410 CNV Insertion 17803354

Variation tolerance for IDH3B Gene

Residual Variation Intolerance Score: 29.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.25; 24.98% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for IDH3B Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IDH3B Gene

Disorders for IDH3B Gene

MalaCards: The human disease database

(3) MalaCards diseases for IDH3B Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 46
  • retinitis pigmentosa autosomal recessive idh3b-related
idh3b-related retinitis pigmentosa
  • retinitis pigmentosa 46
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search IDH3B in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 46 (RP46) [MIM:612572]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:18806796}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for IDH3B

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with IDH3B: view

No data available for Genatlas for IDH3B Gene

Publications for IDH3B Gene

  1. Assignment of mitochondrial NAD(+)-specific isocitrate dehydrogenase beta subunit gene (IDH3B) to human chromosome band 20p13 by in situ hybridization and radiation hybrid mapping. (PMID: 10575215) Kim Y.O. … Huh T.L. (Cytogenet. Cell Genet. 1999) 2 3 23 67
  2. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  5. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta G.D. … Pelletier L. (Cell 2015) 3

Products for IDH3B Gene

Sources for IDH3B Gene