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IDH3B isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta [ Homo sapiens (human) ]

Gene ID: 3420, updated on 11-Apr-2024

Summary

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Official Symbol
IDH3Bprovided by HGNC
Official Full Name
isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit betaprovided by HGNC
Primary source
HGNC:HGNC:5385
See related
Ensembl:ENSG00000101365 MIM:604526; AllianceGenome:HGNC:5385
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RP46
Summary
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]
Expression
Ubiquitous expression in heart (RPKM 34.2), kidney (RPKM 31.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20p13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2658395..2664216, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2688862..2694697, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2639041..2644862, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene NOP56 ribonucleoprotein Neighboring gene MPRA-validated peak4124 silencer Neighboring gene small nucleolar RNA, C/D box 56 Neighboring gene small nucleolar RNA, C/D box 57 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2643139-2643926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2645500-2646285 Neighboring gene IDH3B divergent transcript Neighboring gene uncharacterized LOC105372507

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Polymorphism on chromosome 20p13 near the IDH3B gene is associated with uterine prolapse. Bizjak T, et al. Eur J Obstet Gynecol Reprod Biol, 2020 Sep. PMID 32619879
  2. APC/C-CDH1-Regulated IDH3β Coordinates with the Cell Cycle to Promote Cell Proliferation. Wu Q, et al. Cancer Res, 2019 Jul 1. PMID 31053633
  3. Each conserved active site tyr in the three subunits of human isocitrate dehydrogenase has a different function. Dange M, et al. J Biol Chem, 2010 Jul 2. PMID 20435888, Free PMC Article
  4. Neuro-oncology: Isocitrate dehydrogenase mutations in low-grade gliomas. Schiff D, et al. Nat Rev Neurol, 2009 Jun. PMID 19498431
  5. Regulation of mitochondrial NADP+-dependent isocitrate dehydrogenase activity by glutathionylation. Kil IS, et al. J Biol Chem, 2005 Mar 18. PMID 15653693

See all (87) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Polymorphism on chromosome 20p13 near the IDH3B gene is associated with uterine prolapse.
    Title: Polymorphism on chromosome 20p13 near the IDH3B gene is associated with uterine prolapse.
  2. High IDH3B expression is associated with esophageal squamous cell carcinoma.
    Title: APC/C-CDH1-Regulated IDH3β Coordinates with the Cell Cycle to Promote Cell Proliferation.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  4. Human NAD-dependent isocitrate dehydrogenase (IDH) is a heterotetrameric mitochondrial enzyme with 2alpha:1beta:1gamma subunit ratio subunits shich share 40-52% identity in amino acid sequence.
    Title: Each conserved active site tyr in the three subunits of human isocitrate dehydrogenase has a different function.
  5. The point mutations of isocitrate dehydrogenase are essentially unique to gliomas.
    Title: Neuro-oncology: Isocitrate dehydrogenase mutations in low-grade gliomas.
  6. Homozygous for loss-of-function mutations in IDH3B is associated with retinitis pigmentosa.
    Title: Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle.
  7. IDPm activity appears to be modulated through enzymatic glutathionylation and deglutathionylation during oxidative stress
    Title: Regulation of mitochondrial NADP+-dependent isocitrate dehydrogenase activity by glutathionylation.
  8. active sites of the human NAD-IDH are shared between alpha and gamma subunits and between alpha and beta subunits
    Title: Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase.
  9. Asp192 is needed for optimal affinity of IDH beta subunit for nicotinamide-adenine dinucleotide (NAD) substrate, but is not critical for catalysis.
    Title: Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Retinitis pigmentosa 46
MedGen: C2675496 OMIM: 612572 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC903, FLJ11043

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables NAD binding IEA
Inferred from Electronic Annotation
more info
  
enables electron transfer activity TAS
Traceable Author Statement
more info
 PubMed 
enables isocitrate dehydrogenase (NAD+) activity TAS
Traceable Author Statement
more info
 PubMed 
enables magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in isocitrate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tricarboxylic acid cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tricarboxylic acid cycle IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of isocitrate dehydrogenase complex (NAD+) IPI
Inferred from Physical Interaction
more info
 PubMed 
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 NAS
Non-traceable Author Statement
more info
 PubMed 
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
Names
NAD(+)-specific ICDH subunit beta
isocitrate dehydrogenase (NAD(+)) 3 beta
isocitrate dehydrogenase 3 (NAD(+)) beta
isocitrate dehydrogenase 3 (NAD+) beta
isocitric dehydrogenase subunit beta
NP_001245313.1
NP_001317692.1
NP_008830.2
NP_777280.1

NCBI Reference Sequences (RefSeq)

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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_012149.1 RefSeqGene

    Range
    4982..10803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001258384.3 → NP_001245313.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (d) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK309488, AL049712, HY131986
    Consensus CDS
    CCDS74696.1
    UniProtKB/TrEMBL
    A0A087X2E5
    Related
    ENSP00000484922.1, ENST00000613370.1
    Conserved Domains (1) summary
    cl00445
    Location:47 → 358
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase

  2. NM_001330763.2 → NP_001317692.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform e precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (e) has a longer C-terminus compared to isoform a.
    Source sequence(s)
    BC001960, BX119223, HY131986
    Consensus CDS
    CCDS82594.1
    UniProtKB/TrEMBL
    A0A087WZN1
    Related
    ENSP00000482773.1, ENST00000474315.5

  3. NM_006899.5 → NP_008830.2  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform a precursor

    See identical proteins and their annotated locations for NP_008830.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominate transcript and encodes isoform (a).
    Source sequence(s)
    BC001960, HY131986
    Consensus CDS
    CCDS13032.1
    UniProtKB/Swiss-Prot
    B2RDR1, D3DVX2, D3DVX3, O43837, O95106, Q5JXS8, Q9NQ06, Q9NQ07, Q9NUZ0, Q9UEX0, Q9UG99
    Related
    ENSP00000370223.4, ENST00000380843.9
    Conserved Domains (1) summary
    cl00445
    Location:47 → 380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase

  4. NM_174855.4 → NP_777280.1  isocitrate dehydrogenase [NAD] subunit beta, mitochondrial isoform b precursor

    See identical proteins and their annotated locations for NP_777280.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a portion of the coding region which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    BC001960, BG745042, HY131986
    Consensus CDS
    CCDS13031.1
    UniProtKB/Swiss-Prot
    O43837
    Related
    ENSP00000370232.5, ENST00000380851.9
    Conserved Domains (1) summary
    cl00445
    Location:47 → 380
    Iso_dh; Isocitrate/isopropylmalate dehydrogenase

RNA

  1. NR_136344.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL049712, BX119223, HY131986

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    2658395..2664216 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001754265.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    2688862..2694697 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008485261.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_174856.1: Suppressed sequence

    Description
    NM_174856.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43837.2 GenPept UniProtKB/Swiss-Prot:O43837

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