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    PIP4K2B phosphatidylinositol-5-phosphate 4-kinase type 2 beta [ Homo sapiens (human) ]

    Gene ID: 8396, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PIP4K2Bprovided by HGNC
    Official Full Name
    phosphatidylinositol-5-phosphate 4-kinase type 2 betaprovided by HGNC
    Primary source
    HGNC:HGNC:8998
    See related
    Ensembl:ENSG00000276293 MIM:603261; AllianceGenome:HGNC:8998
    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
    PI5P4KB; PIP5K2B; PIP5KIIB; PIP5P4KB; PIP5KIIbeta
    Summary
    The protein encoded by this gene catalyzes the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. The encoded protein sequence does not show similarity to other kinases, but the protein does exhibit kinase activity. Additionally, the encoded protein interacts with p55 TNF receptor. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 40.4), ovary (RPKM 23.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PIP4K2B in Genome Data Viewer
    Location:
    17q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (38765691..38799556, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (39628767..39662641, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (36921944..36955809, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene tRNA-Asn (anticodon GTT) 2-5 Neighboring gene RNA, U6 small nuclear 866, pseudogene Neighboring gene proteasome 20S subunit beta 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36954986-36955804 Neighboring gene CWC25 spliceosome associated protein homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36980282-36980913 Neighboring gene microRNA 4727

    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. PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1. Poli A, et al. Nat Commun, 2023 Mar 14. PMID 36918565, Free PMC Article
    2. Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. Takeuchi K, et al. FEBS J, 2023 Sep. PMID 36856076, Free PMC Article
    3. PIP4K2B: Coupling GTP Sensing to PtdIns5P Levels to Regulate Tumorigenesis. Fiume R, et al. Trends Biochem Sci, 2016 Jun. PMID 27132569
    4. Phosphoinositide signaling pathways in nuclei are associated with nuclear speckles containing pre-mRNA processing factors. Boronenkov IV, et al. Mol Biol Cell, 1998 Dec. PMID 9843587, Free PMC Article
    5. Overexpression of the amplified Pip4k2beta gene from 17q11-12 in breast cancer cells confers proliferation advantage. Luoh SW, et al. Oncogene, 2004 Feb 19. PMID 14691457

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Functional molecular evolution of a GTP sensing kinase: PI5P4Kbeta.
      Title: Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ.
    2. Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis.
      Title: Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis.
    3. PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1.
      Title: PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1.
    4. Pharmacological inhibition of PI5P4Kalpha/beta disrupts cell energy metabolism and selectively kills p53-null tumor cells.
      Title: Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells.
    5. the loss of PIP4Ks (PIP4K2A, PIP4K2B, and PIP4K2C) in vitro results in a paradoxical increase in PI(4,5)P2 and a concomitant increase in insulin-stimulated production of PI(3,4,5)P3.
      Title: PIP4Ks Suppress Insulin Signaling through a Catalytic-Independent Mechanism.
    6. MiR-3064, a key oncogenic miRNA, could promote PC cell growth, invasion and sphere formation via downregulating the levels of tumor suppressor PIP4K2B.
      Title: Long non-coding RNA PXN-AS1 suppresses pancreatic cancer progression by acting as a competing endogenous RNA of miR-3064 to upregulate PIP4K2B expression.
    7. PIP4K2B couples the cellular GTP concentration to the levels of the stress-regulated phosphoinositide PtdIns5P, to impact on tumor cell growth.
      Title: PIP4K2B: Coupling GTP Sensing to PtdIns5P Levels to Regulate Tumorigenesis.
    8. Suppression of PIP4K expression selectively prevents tumor cell growth in vitro and prevents tumor development in mice that have lost the tumor suppressor p53. (Review)
      Title: PIP4K and the role of nuclear phosphoinositides in tumour suppression.
    9. Association between low PIP4K2B expression and poor patient survival.Analysis of gene expression datasets confirmed the association between low PIP4K2B and low CDH1expression.
      Title: Low PIP4K2B expression in human breast tumors correlates with reduced patient survival: A role for PIP4K2B in the regulation of E-cadherin expression.
    10. Knocking down PI5P4Kalpha and beta in a breast cancer cell line bearing an amplification of the gene encoding PI5P4K beta and deficient for p53 impaired growth on plastic and in xenografts.
      Title: Depletion of a putatively druggable class of phosphatidylinositol kinases inhibits growth of p53-null tumors.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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)

    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 1-phosphatidylinositol-4-phosphate 5-kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 1-phosphatidylinositol-5-phosphate 4-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GTP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in autophagosome-lysosome fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of insulin receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phosphatidylinositol phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in autophagosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phosphatidylinositol 5-phosphate 4-kinase type-2 beta
    Names
    1-phosphatidylinositol 5-phosphate 4-kinase 2-beta
    1-phosphatidylinositol-4-phosphate kinase
    PI(5)P 4-kinase type II beta
    PIP4KII-beta
    PTDINS(4)P-5-kinase
    diphosphoinositide kinase 2-beta
    phosphatidylinositol 5-phosphate 4-kinase type II beta
    phosphatidylinositol-4-phosphate 5-kinase, type II, beta
    NP_003550.1
    XP_011523628.1
    XP_011523629.1
    XP_011523632.1
    XP_047292844.1
    XP_047292845.1
    XP_047292846.1
    XP_054173464.1
    XP_054173465.1
    XP_054173466.1
    XP_054173467.1
    XP_054173468.1
    XP_054173469.1
    XP_054185359.1
    XP_054185360.1
    XP_054185361.1
    XP_054185362.1
    XP_054185363.1
    XP_054185364.1

    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_003559.5 → NP_003550.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta

      See identical proteins and their annotated locations for NP_003550.1

      Status: REVIEWED

      Source sequence(s)
      AC006449, AI333549, U85245
      Consensus CDS
      CCDS11329.1
      UniProtKB/Swiss-Prot
      P78356, Q5U0E8, Q8TBP2
      Related
      ENSP00000482548.1, ENST00000619039.5
      Conserved Domains (1) summary
      cd17310
      Location:30 → 413
      PIPKc_PIP5K2B; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (PIP5K2B) and similar proteins

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      38765691..38799556 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525326.4 → XP_011523628.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X1

      See identical proteins and their annotated locations for XP_011523628.1

      Conserved Domains (1) summary
      cd00139
      Location:39 → 443
      PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...

    2. XM_011525327.3 → XP_011523629.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

      See identical proteins and their annotated locations for XP_011523629.1

      Conserved Domains (1) summary
      cl02572
      Location:1 → 379
      PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...

    3. XM_047436889.1 → XP_047292845.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X3

    4. XM_047436888.1 → XP_047292844.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

    5. XM_011525330.2 → XP_011523632.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X4

      See identical proteins and their annotated locations for XP_011523632.1

      Conserved Domains (1) summary
      cl02572
      Location:39 → 283
      PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...

    6. XM_047436890.1 → XP_047292846.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      2801010..2834875 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329384.1 → XP_054185359.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X1

    2. XM_054329386.1 → XP_054185361.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

    3. XM_054329387.1 → XP_054185362.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X3

    4. XM_054329385.1 → XP_054185360.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

    5. XM_054329388.1 → XP_054185363.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X4

    6. XM_054329389.1 → XP_054185364.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      39628767..39662641 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317489.1 → XP_054173464.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X1

    2. XM_054317491.1 → XP_054173466.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

    3. XM_054317492.1 → XP_054173467.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X3

    4. XM_054317490.1 → XP_054173465.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X2

    5. XM_054317493.1 → XP_054173468.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X4

    6. XM_054317494.1 → XP_054173469.1  phosphatidylinositol 5-phosphate 4-kinase type-2 beta isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_138687.1: Suppressed sequence

      Description
      NM_138687.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78356.1 GenPept UniProtKB/Swiss-Prot:P78356

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