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    IP6K3 inositol hexakisphosphate kinase 3 [ Homo sapiens (human) ]

    Gene ID: 117283, updated on 10-Dec-2024

    Summary

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    Official Symbol
    IP6K3provided by HGNC
    Official Full Name
    inositol hexakisphosphate kinase 3provided by HGNC
    Primary source
    HGNC:HGNC:17269
    See related
    Ensembl:ENSG00000161896 MIM:606993; AllianceGenome:HGNC:17269
    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
    IHPK3; INSP6K3
    Summary
    This gene encodes a protein that belongs to the inositol phosphokinase (IPK) family. This protein is likely responsible for the conversion of inositol hexakisphosphate (InsP6) to diphosphoinositol pentakisphosphate (InsP7/PP-InsP5). It may also convert 1,3,4,5,6-pentakisphosphate (InsP5) to PP-InsP4. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Dec 2008]
    Expression
    Broad expression in thyroid (RPKM 4.4), heart (RPKM 3.1) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IP6K3 in Genome Data Viewer
    Location:
    6p21.31
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33721662..33762145, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33542845..33583325, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33689439..33714682, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33665333-33666308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33672165-33672664 Neighboring gene microRNA 3934 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 2 Neighboring gene uncharacterized LOC124901304 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33678073-33678970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24368 Neighboring gene Sharpr-MPRA regulatory region 11056 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:33692274-33693024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33695430-33696209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33696210-33696988 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33703405-33703659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33710674-33711363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33711622-33712515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33712516-33713408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33713409-33714302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33718585-33719144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33719703-33720261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33728947-33729550 Neighboring gene Sharpr-MPRA regulatory region 8162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33740622-33741320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33747376-33748316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33748317-33749256 Neighboring gene LEM domain nuclear envelope protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33750197-33751135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:33755871-33756420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24369 Neighboring gene uncharacterized LOC105375024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33758333-33758936 Neighboring gene motilin

    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. Contribution of polymorphic variation of inositol hexakisphosphate kinase 3 (IP6K3) gene promoter to the susceptibility to late onset Alzheimer's disease. Crocco P, et al. Biochim Biophys Acta, 2016 Sep. PMID 27345265
    2. IP6K3 and IPMK variations in LOAD and longevity: Evidence for a multifaceted signaling network at the crossroad between neurodegeneration and survival. Dato S, et al. Mech Ageing Dev, 2021 Apr. PMID 33497757
    3. Inositol Hexakisphosphate Kinase 3 Regulates Metabolism and Lifespan in Mice. Moritoh Y, et al. Sci Rep, 2016 Aug 31. PMID 27577108, Free PMC Article
    4. Identification and characterization of a novel inositol hexakisphosphate kinase. Saiardi A, et al. J Biol Chem, 2001 Oct 19. PMID 11502751
    5. Common genetic variants associate with serum phosphorus concentration. Kestenbaum B, et al. J Am Soc Nephrol, 2010 Jul. PMID 20558539, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IP6K3 and IPMK variations in LOAD and longevity: Evidence for a multifaceted signaling network at the crossroad between neurodegeneration and survival.
      Title: IP6K3 and IPMK variations in LOAD and longevity: Evidence for a multifaceted signaling network at the crossroad between neurodegeneration and survival.
    2. Two SNPs in the 5'-flanking promoter region of the IP6K3 gene were found to be associated with sporadic late onset Alzheimer's disease. Characterizing the functionality of the two polymorphisms by luciferase assay revealed that one of them (rs28607030) affects IP6K3 promoter activity, with the G allele showing an increased activity.
      Title: Contribution of polymorphic variation of inositol hexakisphosphate kinase 3 (IP6K3) gene promoter to the susceptibility to late onset Alzheimer's disease.
    3. High levels of IP6K3 mRNA were found in myotubes and muscle tissues. In myotubes, IP6K3 was upregulated by dexamethasone treatment, which is known to inhibit glucose metabolism.
      Title: Inositol Hexakisphosphate Kinase 3 Regulates Metabolism and Lifespan in Mice.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    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
    Common genetic variants associate with serum phosphorus concentration.
    EBI GWAS Catalog
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    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)

    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

    • MGC102928

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diphosphoinositol pentakisphosphate kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables diphosphoinositol tetrakisphosphate kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables inositol 5-diphosphate pentakisphosphate 5-kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables inositol hexakisphosphate 1-kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol hexakisphosphate 5-kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol hexakisphosphate 6-kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables inositol hexakisphosphate kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol hexakisphosphate kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables inositol hexakisphosphate kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables inositol-1,3,4,5,6-pentakisphosphate kinase activity TAS
    Traceable Author Statement
    more info
    		  
    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
    		  
    acts_upstream_of_or_within inositol phosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in inositol phosphate metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in locomotion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylinositol phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol 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 hexakisphosphate kinase 3
    Names
    ATP:1D-myo-inositol-hexakisphosphate phosphotransferase
    InsP6 kinase 3
    inositol hexaphosphate kinase 3
    NP_001136355.1
    NP_473452.2
    XP_005248899.1
    XP_005248900.1
    XP_011512597.1
    XP_024302091.1
    XP_024302092.1
    XP_024302093.1
    XP_047274124.1
    XP_054210172.1
    XP_054210173.1
    XP_054210174.1
    XP_054210175.1
    XP_054210176.1
    XP_054210177.1

    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.

    mRNA and Protein(s)

    1. NM_001142883.2 → NP_001136355.1  inositol hexakisphosphate kinase 3

      See identical proteins and their annotated locations for NP_001136355.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AK289935, AL139044, BC089389
      Consensus CDS
      CCDS34435.1
      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Related
      ENSP00000398861.1, ENST00000451316.6
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    2. NM_054111.5 → NP_473452.2  inositol hexakisphosphate kinase 3

      See identical proteins and their annotated locations for NP_473452.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript.
      Source sequence(s)
      AK289935, AL139044, BC089389
      Consensus CDS
      CCDS34435.1
      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Related
      ENSP00000293756.4, ENST00000293756.5
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33721662..33762145 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446324.2 → XP_024302092.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    2. XM_024446325.2 → XP_024302093.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    3. XM_047418168.1 → XP_047274124.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4

    4. XM_011514295.4 → XP_011512597.1  inositol hexakisphosphate kinase 3 isoform X3

      Conserved Domains (1) summary
      cl12283
      Location:198 → 256
      IPK; Inositol polyphosphate kinase

    5. XM_005248842.4 → XP_005248899.1  inositol hexakisphosphate kinase 3 isoform X1

      See identical proteins and their annotated locations for XP_005248899.1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    6. XM_024446323.2 → XP_024302091.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4
      Conserved Domains (1) summary
      pfam03770
      Location:198 → 404
      IPK; Inositol polyphosphate kinase

    7. XM_005248843.5 → XP_005248900.1  inositol hexakisphosphate kinase 3 isoform X2

      Conserved Domains (1) summary
      pfam03770
      Location:85 → 291
      IPK; Inositol polyphosphate kinase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33542845..33583325 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354198.1 → XP_054210173.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4

    2. XM_054354200.1 → XP_054210175.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4

    3. XM_054354202.1 → XP_054210177.1  inositol hexakisphosphate kinase 3 isoform X3

    4. XM_054354199.1 → XP_054210174.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4

    5. XM_054354197.1 → XP_054210172.1  inositol hexakisphosphate kinase 3 isoform X1

      UniProtKB/Swiss-Prot
      Q96MQ9, Q96PC2
      UniProtKB/TrEMBL
      A8K1M0, Q53ER7, Q5TAQ4

    6. XM_054354201.1 → XP_054210176.1  inositol hexakisphosphate kinase 3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96PC2.2 GenPept UniProtKB/Swiss-Prot:Q96PC2

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