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    IDH2 isocitrate dehydrogenase (NADP(+)) 2 [ Homo sapiens (human) ]

    Gene ID: 3418, updated on 3-Nov-2024

    Summary

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    Official Symbol
    IDH2provided by HGNC
    Official Full Name
    isocitrate dehydrogenase (NADP(+)) 2provided by HGNC
    Primary source
    HGNC:HGNC:5383
    See related
    Ensembl:ENSG00000182054 MIM:147650; AllianceGenome:HGNC:5383
    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
    IDH; IDP; IDHM; IDPM; ICD-M; IDH-2; D2HGA2; mNADP-IDH
    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. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the mitochondria. It plays a role in intermediary metabolism and energy production. This protein may tightly associate or interact with the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
    Expression
    Ubiquitous expression in heart (RPKM 100.1), kidney (RPKM 92.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IDH2 in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90083045..90102468, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87839072..87858500, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90626277..90645700, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 710 Neighboring gene microRNA 3174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90581285-90581804 Neighboring gene Sharpr-MPRA regulatory region 12348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90585951-90586930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90597371-90598254 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90602135-90602846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6809 Neighboring gene ZNF710 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90627210-90627710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90627711-90628211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90630317-90631230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90634376-90634876 Neighboring gene NANOG hESC enhancer GRCh37_chr15:90638658-90639182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644126-90644981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644982-90645836 Neighboring gene IDH2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90664819-90665318 Neighboring gene Sharpr-MPRA regulatory region 4454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90686773-90687307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701094-90701611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701612-90702128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704142-90704734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704735-90705327 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90707039-90707194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90717667-90718167 Neighboring gene RNA, 7SL, cytoplasmic 346, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90721295-90722200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90727462-90728195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90744110-90745081 Neighboring gene semaphorin 4B Neighboring gene ribosomal protein S12 pseudogene 26

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IDH2 regulates U2AF1 expression and hydroxymethylation in MDS patients.
      Title: IDH2 regulates U2AF1 expression and hydroxymethylation in MDS patients.
    2. Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma.
      Title: Differential isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 mutation-related landscape in intrahepatic cholangiocarcinoma.
    3. Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2).
      Title: Epigenetic dysregulation in cancers by isocitrate dehydrogenase 2 (IDH2).
    4. Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma.
      Title: Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma.
    5. IDH2/R140Q mutation confers cytokine-independent proliferation of TF-1 cells by activating constitutive STAT3/5 phosphorylation.
      Title: IDH2/R140Q mutation confers cytokine-independent proliferation of TF-1 cells by activating constitutive STAT3/5 phosphorylation.
    6. Isocitrate dehydrogenase 2 regulates the proliferation of triple-negative breast cancer through the ferroptosis pathway.
      Title: Isocitrate dehydrogenase 2 regulates the proliferation of triple-negative breast cancer through the ferroptosis pathway.
    7. Clinical and imaging characteristics of supratentorial glioma with IDH2 mutation.
      Title: Clinical and imaging characteristics of supratentorial glioma with IDH2 mutation.
    8. Genetic Polymorphism Study of IDH 1/2 and TET2 Genes in Acute Myeloid leukemia Patients.
      Title: Genetic Polymorphism Study of IDH 1/2 and TET2 Genes in Acute Myeloid leukemia Patients.
    9. IDH2 mutations in acute myeloid leukemia.
      Title: IDH2 mutations in acute myeloid leukemia.
    10. The impact of IDH and NAT2 gene polymorphisms in acute myeloid leukemia risk and overall survival in an Arab population: A case-control study.
      Title: The impact of IDH and NAT2 gene polymorphisms in acute myeloid leukemia risk and overall survival in an Arab population: A case-control study.
    Submit: New GeneRIF Correction See all GeneRIFs (406)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    D-2-hydroxyglutaric aciduria 2
    MedGen: C3150909 OMIM: 613657 GeneReviews: Not available
    		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)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of isocitrate dehydrogenase 2 (IDH2) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables isocitrate dehydrogenase (NADP+) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables isocitrate dehydrogenase (NADP+) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables isocitrate dehydrogenase (NADP+) activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables isocitrate dehydrogenase (NADP+) activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables magnesium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in 2-oxoglutarate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in NADP metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in carbohydrate metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in glyoxylate cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in isocitrate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in tricarboxylic acid cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HDA PubMed 
    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 peroxisome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    isocitrate dehydrogenase [NADP], mitochondrial
    Names
    NADP(+)-specific ICDH
    isocitrate dehydrogenase (NADP(+)) 2, mitochondrial
    isocitrate dehydrogenase 2 (NADP+), mitochondrial
    oxalosuccinate decarboxylase
    NP_001276839.1
    NP_001277043.1
    NP_002159.2

    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_023302.1 RefSeqGene

      Range
      4923..23499
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_611

    mRNA and Protein(s)

    1. NM_001289910.1 → NP_001276839.1  isocitrate dehydrogenase [NADP], mitochondrial isoform 2

      See identical proteins and their annotated locations for NP_001276839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK294148, BC009244
      Consensus CDS
      CCDS76792.1
      UniProtKB/TrEMBL
      Q53GL5
      Related
      ENSP00000446147.2, ENST00000540499.2
      Conserved Domains (1) summary
      PTZ00435
      Location:1 → 399
      PTZ00435; isocitrate dehydrogenase; Provisional

    2. NM_001290114.2 → NP_001277043.1  isocitrate dehydrogenase [NADP], mitochondrial isoform 3

      See identical proteins and their annotated locations for NP_001277043.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC087284, AK299987, X69433
      UniProtKB/TrEMBL
      B4DSZ6
      Conserved Domains (1) summary
      cl00445
      Location:1 → 321
      Iso_dh; Isocitrate/isopropylmalate dehydrogenase

    3. NM_002168.4 → NP_002159.2  isocitrate dehydrogenase [NADP], mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_002159.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC087284, AK312627, X69433
      Consensus CDS
      CCDS10359.1
      UniProtKB/Swiss-Prot
      B2R6L6, B4DFL2, P48735, Q96GT3
      UniProtKB/TrEMBL
      Q53GL5
      Related
      ENSP00000331897.4, ENST00000330062.8
      Conserved Domains (1) summary
      PTZ00435
      Location:39 → 451
      PTZ00435; isocitrate dehydrogenase; Provisional

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      90083045..90102468 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      87839072..87858500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P48735.2 GenPept UniProtKB/Swiss-Prot:P48735

    Gene LinkOut

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

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