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Aliases for IDH3B Gene

Aliases for IDH3B Gene

  • Isocitrate Dehydrogenase 3 (NAD(+)) Beta 2 3 5
  • Isocitrate Dehydrogenase 3 (NAD+) Beta 2 3
  • Isocitric Dehydrogenase Subunit Beta 3 4
  • NAD(+)-Specific ICDH Subunit Beta 3 4
  • EC 4 61
  • Isocitrate Dehydrogenase [NAD] Subunit Beta, Mitochondrial 3
  • EC 1.1.1 61
  • 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. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2016]

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 Pyruvate metabolism and Citric Acid (TCA) cycle and Carbon metabolism. 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 CIViC summary , 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 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
GH20G002651 1.1 ENCODE 23.6 +11.0 11014 4.2 HDGF HNRNPUL1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 IDH3B ZNF343 VPS16 ITPA NOP56 GC20P002854 MIR1292
GH20G002658 0.8 ENCODE 15.7 +5.3 5280 0.3 INSM2 BACH1 KLF17 CDC5L CHD7 GLIS2 ZNF354C POLR2A ZNF547 PATZ1 IDH3B ZNF343 NOP56 SNORD57
GH20G002507 1.1 ENCODE 10.3 +155.4 155449 2.6 PKNOX1 FOXA2 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF343 SNRPB TMC2 NOP56 SNORD56 SNORD57 ENSG00000228293 IDH3B ENSG00000256566 GC20M002474
GH20G002740 0.8 ENCODE 10.9 -77.7 -77738 2.3 CTCF DRAP1 ARID4B RAD21 HBP1 ZNF48 GLIS2 ZBTB48 ZNF143 EZH2 EBF4 VPS16 PTPRA PCED1A ENSG00000241690 TMEM239 C20orf141 IDH3B ENSG00000228293 NOP56
GH20G002663 1.1 ENCODE 6.9 +0.1 85 1.9 PKNOX1 MLX ZFP64 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 ZNF343 NOP56 IDH3B SNORD57
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000133686 19 1201 PKNOX1 MLX ZFP64 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207

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

Selected DME Specific Peptides for IDH3B Gene


Post-translational modifications for IDH3B Gene

  • Ubiquitination at posLast=199199
  • Modification sites at PhosphoSitePlus

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

Gene Ontology (GO) - Molecular Function for IDH3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IEA --
GO:0004449 isocitrate dehydrogenase (NAD+) activity IEA --
GO:0009055 electron carrier activity TAS 10601238
GO:0016491 oxidoreductase activity IEA --
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA --
genes like me logo Genes that share ontologies with IDH3B: view
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

CRISPR Products

Inhibitory RNA Products

No data available for 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

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 IDH3B gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for IDH3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005739 mitochondrion IDA,IEA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with IDH3B: view

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:0006102 isocitrate metabolic process TAS 10601238
GO:0006103 2-oxoglutarate metabolic process IEA --
GO:0006734 NADH metabolic process IEA --
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

(6) Drugs for IDH3B 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 IDH3B 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 IDH3B: view

Transcripts for IDH3B Gene

Unigene Clusters for IDH3B Gene

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

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for IDH3B Gene

Protein tissue co-expression partners for IDH3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of IDH3B Gene:


SOURCE GeneReport for Unigene cluster for IDH3B Gene:


Evidence on tissue expression from TISSUES for IDH3B Gene

  • Heart(4.6)
  • Lung(4.6)
  • Nervous system(4.6)
  • Liver(3.1)
  • Skin(2.8)
  • Muscle(2.7)
  • Intestine(2.5)
  • Blood(2.3)
  • Eye(2.3)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for IDH3B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with IDH3B: view

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
(Pan troglodytes)
Mammalia IDH3B 34 35
  • 99.83 (n)
(Canis familiaris)
Mammalia -- 35
  • 96 (a)
IDH3B 34
  • 92.01 (n)
-- 35
  • 74 (a)
(Bos Taurus)
Mammalia IDH3B 34 35
  • 92.19 (n)
(Monodelphis domestica)
Mammalia -- 35
  • 91 (a)
-- 35
  • 74 (a)
(Rattus norvegicus)
Mammalia Idh3B 34
  • 90.02 (n)
(Mus musculus)
Mammalia Idh3b 34 16 35
  • 88.34 (n)
(Gallus gallus)
Aves IDH3B 34 35
  • 78.51 (n)
(Anolis carolinensis)
Reptilia IDH3B 35
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia idh3b 34
  • 76.79 (n)
Str.8848 34
(Danio rerio)
Actinopterygii idh3b 34 35
  • 74.88 (n)
Dr.12046 34
fruit fly
(Drosophila melanogaster)
Insecta CG6439 36 34 35
  • 64.3 (n)
CG5028 36
  • 43 (a)
CG3483 36
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007786 34
  • 61.13 (n)
(Caenorhabditis elegans)
Secernentea idhb-1 34 35
  • 60.55 (n)
C37E2.1 36
  • 60 (a)
F35G12.2 36
  • 47 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL223W 34
  • 56.16 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04103g 34
  • 54.65 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IDH1 34 35
  • 51.81 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons IDH2 34
  • 56.91 (n)
(Oryza sativa)
Liliopsida Os04g0479200 34
  • 55.04 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7868 35
  • 61 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00775 34
  • 55.59 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes idh1 34
  • 52.69 (n)
Species where no ortholog for IDH3B 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)
  • 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
rs137853020 Pathogenic, Retinitis pigmentosa 46 (RP46) [MIM:612572] 2,660,912(-) GCGGC(C/T)GAGGT nc-transcript-variant, reference, missense
rs5856 Likely benign 2,658,236(+) GGCGG(C/T)TGGCA intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs6753 Likely benign 2,657,933(+) GGAGA(C/T)GAGTG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs8296 Likely benign 2,658,516(-) TTCGA(A/G)CCTCT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense, utr-variant-3-prime
rs139159095 Uncertain significance 2,663,531(+) CTCAG(A/G)TGGTG nc-transcript-variant, reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
esv1188410 CNV insertion 17803354
esv3644998 CNV gain 21293372
esv988063 CNV insertion 20482838
nsv1057464 CNV gain 25217958
nsv458852 CNV loss 19166990
nsv470535 CNV gain 18288195
nsv585266 CNV loss 21841781

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for IDH3B Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
retinitis pigmentosa 46
  • rp46
idh3b-related retinitis pigmentosa
  • retinitis pigmentosa 46
retinitis pigmentosa
  • retinitis pigmentosa 1
retinitis pigmentosa 28
  • rp28
- 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 22 64
  2. 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
  3. Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle. (PMID: 18806796) Hartong D.T. … Colman R.F. (Nat. Genet. 2008) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. 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

Products for IDH3B Gene

Sources for IDH3B Gene

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