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

    Gene ID: 3420, updated on 10-Dec-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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    See IDH3B in Genome Data Viewer
    Location:
    20p13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2658395..2664216, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2688862..2694697, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    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. Kim YO, et al. Cytogenet Cell Genet, 1999. PMID 10575215
    2. Regulation of mitochondrial NADP+-dependent isocitrate dehydrogenase activity by glutathionylation. Kil IS, et al. J Biol Chem, 2005 Mar 18. PMID 15653693
    3. Neuro-oncology: Isocitrate dehydrogenase mutations in low-grade gliomas. Schiff D, et al. Nat Rev Neurol, 2009 Jun. PMID 19498431
    4. 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
    5. 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

    See all (101) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A positive feedback inhibition of isocitrate dehydrogenase 3beta on paired-box gene 6 promotes Alzheimer-like pathology.
      Title: A positive feedback inhibition of isocitrate dehydrogenase 3β on paired-box gene 6 promotes Alzheimer-like pathology.
    2. 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.
    3. 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.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    5. 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.
    6. The point mutations of isocitrate dehydrogenase are essentially unique to gliomas.
      Title: Neuro-oncology: Isocitrate dehydrogenase mutations in low-grade gliomas.
    7. 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.
    8. 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.
    9. 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.
    10. 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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+) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of isocitrate dehydrogenase complex (NAD+) IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    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, ENST00000380851.10
      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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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