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

Gene ID: 8396, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (38765691..38799556, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (39628767..39662641, complement)
105.20220307 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: 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. 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. PIP4K2B: Coupling GTP Sensing to PtdIns5P Levels to Regulate Tumorigenesis. Fiume R, et al. Trends Biochem Sci, 2016 Jun. PMID 27132569
  3. 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
  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. Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis. Geroldinger-Simić M, et al. Int J Mol Sci, 2023 Mar 15. PMID 36982700, Free PMC Article

See all (65) 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)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 1-phosphatidylinositol-4-phosphate 5-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 phosphorylation IEA
Inferred from Electronic Annotation
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_2023_10

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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