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    IDH1 isocitrate dehydrogenase (NADP(+)) 1 [ Homo sapiens (human) ]

    Gene ID: 3417, updated on 28-Oct-2024

    Summary

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    Official Symbol
    IDH1provided by HGNC
    Official Full Name
    isocitrate dehydrogenase (NADP(+)) 1provided by HGNC
    Primary source
    HGNC:HGNC:5382
    See related
    Ensembl:ENSG00000138413 MIM:147700; AllianceGenome:HGNC:5382
    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; IDCD; IDPC; PICD; HEL-216; HEL-S-26
    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 cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]
    Expression
    Ubiquitous expression in adrenal (RPKM 116.0), liver (RPKM 110.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IDH1 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (208236227..208255071, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (208716002..208734866, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (209100951..209119795, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:209080668-209081230 Neighboring gene ribosomal protein SA pseudogene 27 Neighboring gene TPT1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12288 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:209119503-209120029 Neighboring gene IDH1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17051 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:209134199-209134700 Neighboring gene phosphoinositide kinase, FYVE-type zinc finger containing Neighboring gene MYL6B pseudogene 1

    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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    Related articles in PubMed

    1. IDH1 mutation of gliomas with long-term survival analysis. Myung JK, et al. Oncol Rep, 2012 Nov. PMID 22922798
    2. Functional requirement of a wild-type allele for mutant IDH1 to suppress anchorage-independent growth through redox homeostasis. Tiburcio PDB, et al. Acta Neuropathol, 2018 Feb. PMID 29288440
    3. IDH1R132H Promotes Malignant Transformation of Benign Prostatic Epithelium by Dysregulating MicroRNAs: Involvement of IGF1R-AKT/STAT3 Signaling Pathway. Zhang L, et al. Neoplasia, 2018 Feb. PMID 29331887, Free PMC Article
    4. IDH1 mutations in oligodendroglial tumors: comparative analysis of direct sequencing, pyrosequencing, immunohistochemistry, nested PCR and PNA-mediated clamping PCR. Lee D, et al. Brain Pathol, 2013 May. PMID 23072665, Free PMC Article
    5. Extent of BOLD Vascular Dysregulation Is Greater in Diffuse Gliomas without Isocitrate Dehydrogenase 1 R132H Mutation. Englander ZK, et al. Radiology, 2018 Jun. PMID 29369751

    See all (973) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Gaining Insight into the Catalytic Mechanism of the R132H IDH1 Mutant: A Synergistic DFT Cluster and Experimental Investigation.
      Title: Gaining Insight into the Catalytic Mechanism of the R132H IDH1 Mutant: A Synergistic DFT Cluster and Experimental Investigation.
    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. The interplay mechanism between IDH mutation, MGMT-promoter methylation, and PRMT5 activity in the progression of grade 4 astrocytoma: unraveling the complex triad theory.
      Title: The interplay mechanism between IDH mutation, MGMT-promoter methylation, and PRMT5 activity in the progression of grade 4 astrocytoma: unraveling the complex triad theory.
    4. IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma.
      Title: IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma.
    5. Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity.
      Title: Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity.
    6. Demographic bias in misdiagnosis by computational pathology models.
      Title: Demographic bias in misdiagnosis by computational pathology models.
    7. Correlation of IDH1 gene expression error in breast tumor biopsy in patients with invasive ductal carcinoma.
      Title: Correlation of IDH1 gene expression error in breast tumor biopsy in patients with invasive ductal carcinoma.
    8. IDH1 p.R132C mutation in prostatic carcinoma with psammomatous calcifications: report of two cases.
      Title: IDH1 p.R132C mutation in prostatic carcinoma with psammomatous calcifications: report of two cases.
    9. IDH1[R132H] mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas.
      Title: IDH1(R132H) mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas.
    10. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.
      Title: The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.
    Submit: New GeneRIF Correction See all GeneRIFs (892)

    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
    Glioma susceptibility 1
    MedGen: C2750850 OMIM: 137800 GeneReviews: Not available
    		not available

    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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    Replication interactions

    Interaction Pubs
    Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
    Knockdown of isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 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 NADP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cadherin binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in 2-oxoglutarate metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in NADP metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in female gonad development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glutathione metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glyoxylate cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in isocitrate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in isocitrate metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of phospholipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of phospholipid catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to oxidative stress IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to steroid hormone IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tricarboxylic acid cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in peroxisomal matrix TAS
    Traceable Author Statement
    more info
    		  
    is_active_in peroxisome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in tertiary granule lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    isocitrate dehydrogenase [NADP] cytoplasmic
    Names
    NADP(+)-specific ICDH
    NADP-dependent isocitrate dehydrogenase, cytosolic
    NADP-dependent isocitrate dehydrogenase, peroxisomal
    epididymis luminal protein 216
    epididymis secretory protein Li 26
    epididymis secretory sperm binding protein
    isocitrate dehydrogenase (NADP(+)) 1, cytosolic
    isocitrate dehydrogenase 1 (NADP+), soluble
    oxalosuccinate decarboxylase
    NP_001269315.1
    NP_001269316.1
    NP_005887.2

    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_023319.2 RefSeqGene

      Range
      15932..34848
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_610

    mRNA and Protein(s)

    1. NM_001282386.1 → NP_001269315.1  isocitrate dehydrogenase [NADP] cytoplasmic

      See identical proteins and their annotated locations for NP_001269315.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      BC021046, DA707595, N21575
      Consensus CDS
      CCDS2381.1
      UniProtKB/Swiss-Prot
      O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8
      UniProtKB/TrEMBL
      A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2
      Related
      ENSP00000410513.1, ENST00000446179.5
      Conserved Domains (1) summary
      PTZ00435
      Location:1 → 411
      PTZ00435; isocitrate dehydrogenase; Provisional

    2. NM_001282387.1 → NP_001269316.1  isocitrate dehydrogenase [NADP] cytoplasmic

      See identical proteins and their annotated locations for NP_001269316.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate 5' UTR exon, compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      BC012846, DR158630, N21575
      Consensus CDS
      CCDS2381.1
      UniProtKB/Swiss-Prot
      O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8
      UniProtKB/TrEMBL
      A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2
      Related
      ENSP00000390265.1, ENST00000415913.5
      Conserved Domains (1) summary
      PTZ00435
      Location:1 → 411
      PTZ00435; isocitrate dehydrogenase; Provisional

    3. NM_005896.4 → NP_005887.2  isocitrate dehydrogenase [NADP] cytoplasmic

      See identical proteins and their annotated locations for NP_005887.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) and variants 2 and 3 encode the same protein.
      Source sequence(s)
      AC016697, BC021046, DA728868
      Consensus CDS
      CCDS2381.1
      UniProtKB/Swiss-Prot
      O75874, Q567U4, Q6FHQ6, Q7Z3V0, Q93090, Q9NTJ9, Q9UKW8
      UniProtKB/TrEMBL
      A0A024R3Y6, B2R5M8, Q6FI37, V9HWJ2
      Related
      ENSP00000260985.2, ENST00000345146.7
      Conserved Domains (1) summary
      PTZ00435
      Location:1 → 411
      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      208236227..208255071 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      208716002..208734866 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75874.2 GenPept UniProtKB/Swiss-Prot:O75874

    Gene LinkOut

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

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