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    IPPK inositol-pentakisphosphate 2-kinase [ Homo sapiens (human) ]

    Gene ID: 64768, updated on 5-Mar-2024

    Summary

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    Official Symbol
    IPPKprovided by HGNC
    Official Full Name
    inositol-pentakisphosphate 2-kinaseprovided by HGNC
    Primary source
    HGNC:HGNC:14645
    See related
    Ensembl:ENSG00000127080 MIM:619043; AllianceGenome:HGNC:14645
    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
    IP5K; IPK1; C9orf12; INSP5K2; bA476B13.1
    Summary
    The protein encoded by this gene is a kinase that phosphorylates position 2 of inositol-1,3,4,5,6-pentakisphosphate to form inositol-1,2,3,4,5,6-hexakisphosphate (InsP6). InsP6 has a variety of functions, including stimulation of DNA repair, endocytosis, and mRNA export. [provided by RefSeq, Nov 2010]
    Expression
    Ubiquitous expression in skin (RPKM 15.1), esophagus (RPKM 8.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q22.31
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (92613183..92670131, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104779754..104836695, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95375465..95432413, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene centromere protein P Neighboring gene asporin Neighboring gene extracellular matrix protein 2 Neighboring gene Sharpr-MPRA regulatory region 3268 Neighboring gene microRNA 4670 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:95320296-95321495 Neighboring gene uncharacterized LOC100128361 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:95383063-95383333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28597 Neighboring gene uncharacterized LOC107987095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28598 Neighboring gene Sharpr-MPRA regulatory region 2132 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109781 Neighboring gene ribosomal protein L21 pseudogene 86

    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. Urine inositol pentakisphosphate 2-kinase and changes in kidney structure in early diabetic kidney disease in type 1 diabetes. Looker HC, et al. Am J Physiol Renal Physiol, 2018 Nov 1. PMID 30132343, Free PMC Article
    2. Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity. Gosein V, et al. J Biol Chem, 2013 Dec 27. PMID 24165122, Free PMC Article
    3. Physiological levels of PTEN control the size of the cellular Ins(1,3,4,5,6)P(5) pool. Deleu S, et al. Cell Signal, 2006 Apr. PMID 15979280
    4. Depletion of mRNA export regulator DBP5/DDX19, GLE1 or IPPK that is a key enzyme for the production of IP6, resulting in differentially altered cytoplasmic mRNA expression and specific cell defect. Okamura M, et al. PLoS One, 2018. PMID 29746542, Free PMC Article
    5. Increased levels of inositol hexakisphosphate (InsP6) protect HEK293 cells from tumor necrosis factor (alpha)- and Fas-induced apoptosis. Verbsky J, et al. J Biol Chem, 2005 Aug 12. PMID 15967797

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Higher urine IPP2K/Cr is associated with less severe kidney lesions at baseline and with preservation of kidney structure over 5 yr in individuals with type 1 diabetes and no clinical evidence of DKD at baseline.
      Title: Urine inositol pentakisphosphate 2-kinase and changes in kidney structure in early diabetic kidney disease in type 1 diabetes.
    2. These results imply that DBP5, GLE1 and IP6 have a conserved and individual function in the cytoplasmic mRNA expression. Variations in phenotype are due to the difference in each function of DBP5, GLE1 and IPPK in intracellular mRNA metabolism.
      Title: Depletion of mRNA export regulator DBP5/DDX19, GLE1 or IPPK that is a key enzyme for the production of IP6, resulting in differentially altered cytoplasmic mRNA expression and specific cell defect.
    3. IP6 synthase, Ins(1,3,4,5,6)P5 2-kinase (IPPK/IP5K) binds to cullins. Depleting IP5K increases the percentage of neddylated, active Cul1 and Cul4A, and decreases levels of the Cul1/4A substrates p27 and p21.
      Title: Inositol hexakisphosphate (IP6) generated by IP5K mediates cullin-COP9 signalosome interactions and CRL function.
    4. IPK1 substrate selection is linked to the ability of each potential substrate to stabilize IPK1.
      Title: Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity.
    5. identified a genomic DNA sequence on chromosome 9 that encodes inositol 1,3,4,5,6-pentakisphosphate 2-kinase; characterization of the enzyme
      Title: The synthesis of inositol hexakisphosphate. Characterization of human inositol 1,3,4,5,6-pentakisphosphate 2-kinase.
    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

    EBI GWAS Catalog

    Description
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    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

    • FLJ13163, KIAA0699

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol pentakisphosphate 2-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol pentakisphosphate 2-kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables inositol pentakisphosphate 2-kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables molecular adaptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in inositol phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inositol phosphate metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleolus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    inositol-pentakisphosphate 2-kinase
    Names
    IPK1 homolog
    inositol 1,3,4,5,6-pentakisphosphate 2-kinase
    ins(1,3,4,5,6)P5 2-kinase
    insP5 2-kinase
    NP_073592.1
    XP_016870530.1
    XP_047279688.1
    XP_054219529.1
    XP_054219530.1

    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_027879.1 RefSeqGene

      Range
      5135..62083
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_022755.6 → NP_073592.1  inositol-pentakisphosphate 2-kinase

      See identical proteins and their annotated locations for NP_073592.1

      Status: REVIEWED

      Source sequence(s)
      AL157827, BC026154
      Consensus CDS
      CCDS6699.1
      UniProtKB/Swiss-Prot
      Q5T9F7, Q9H7V8, Q9H8X2
      Related
      ENSP00000287996.3, ENST00000287996.8
      Conserved Domains (1) summary
      pfam06090
      Location:13 → 455
      Ins_P5_2-kin; Inositol-pentakisphosphate 2-kinase

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      92613183..92670131 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017015041.2 → XP_016870530.1  inositol-pentakisphosphate 2-kinase isoform X1

    2. XM_047423732.1 → XP_047279688.1  inositol-pentakisphosphate 2-kinase isoform X2

      UniProtKB/TrEMBL
      X6R9A6
      Related
      ENSP00000364672.2, ENST00000375522.2

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791788.1 Reference GRCh38.p14 PATCHES

      Range
      447910..477543 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      104779754..104836695 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363554.1 → XP_054219529.1  inositol-pentakisphosphate 2-kinase isoform X1

    2. XM_054363555.1 → XP_054219530.1  inositol-pentakisphosphate 2-kinase isoform X2

      UniProtKB/TrEMBL
      X6R9A6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H8X2.1 GenPept UniProtKB/Swiss-Prot:Q9H8X2

    Gene LinkOut

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

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