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PI4K2B phosphatidylinositol 4-kinase type 2 beta [ Homo sapiens (human) ]

Gene ID: 55300, updated on 6-Jun-2024

Summary

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Official Symbol
PI4K2Bprovided by HGNC
Official Full Name
phosphatidylinositol 4-kinase type 2 betaprovided by HGNC
Primary source
HGNC:HGNC:18215
See related
Ensembl:ENSG00000038210 MIM:612101; AllianceGenome:HGNC:18215
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
PIK42B; PI4KIIB
Summary
This gene encodes a member of the type II PI4 kinase protein family. The encoded protein is primarily cytosolic and contributes to overall PI4-kinase activity along with other protein family members. This protein is involved in early T cell activation. [provided by RefSeq, Dec 2016]
Expression
Ubiquitous expression in duodenum (RPKM 18.2), small intestine (RPKM 15.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PI4K2B in Genome Data Viewer
Location:
4p15.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (25234033..25279204)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (25215954..25261023)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (25235655..25280826)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133175-25133701 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133702-25134228 Neighboring gene Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21370 Neighboring gene SEPSECS antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21371 Neighboring gene uncharacterized LOC105374535 Neighboring gene H3K27ac hESC enhancers GRCh37_chr4:25235481-25235982 and GRCh37_chr4:25235983-25236482 Neighboring gene uncharacterized LOC124900916 Neighboring gene uncharacterized LOC124900685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25314050-25314926 Neighboring gene uncharacterized LOC124900686 Neighboring gene zinc finger CCHC-type containing 4

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. Type II PtdIns 4-kinase β associates with CD4-p56lck complex and is involved in CD4 receptor signaling. Sinha RK, et al. Mol Cell Biochem, 2014 Oct. PMID 24972704
  2. Type II phosphatidylinositol 4-kinase β is an integral signaling component of early T cell activation mechanisms. Sinha RK, et al. Biochimie, 2013 Aug. PMID 23619705
  3. A case-control association study and family-based expression analysis of the bipolar disorder candidate gene PI4K2B. Houlihan LM, et al. J Psychiatr Res, 2009 Dec. PMID 19539307, Free PMC Article
  4. Identification of phosphatidylinositol 4-kinase type II beta as HLA class II-restricted target in graft versus leukemia reactivity. Griffioen M, et al. Proc Natl Acad Sci U S A, 2008 Mar 11. PMID 18316730, Free PMC Article
  5. The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design. Klima M, et al. Acta Crystallogr D Biol Crystallogr, 2015 Jul. PMID 26143926

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNA interference of the type II phosphatidylinositol 4-kinases PI4KIIa and PI4KIIa in primary human endothelial cells leads to formation of an increased proportion of short WPB with perturbed packing of VWF, as exemplified by increased exposure of antibody-binding sites.
    Title: Type II PI4-kinases control Weibel-Palade body biogenesis and von Willebrand factor structure in human endothelial cells.
  2. Here two crystal structures are presented: the structure of human PIK42A and the structure of PIK42B containing a nucleoside analogue.
    Title: The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design.
  3. Results provide evidence that type II PtdIns 4-kinase b was indeed recruited to CD4- p56lck complex upon CD4 receptor cross linking, suggests a mechanism for its association and a role for it in CD4-mediated intracellular calcium release.
    Title: Type II PtdIns 4-kinase β associates with CD4-p56lck complex and is involved in CD4 receptor signaling.
  4. Canonical tyrosine residues mutation in FcepsilonRIgamma ITAM (Y65 and Y76) reveals that these two tyrosine residues in gamma subunit are required for its interaction with type II PtdIns 4-kinases.
    Title: Type II phosphatidylinositol 4-kinases interact with FcεRIγ subunit in RBL-2H3 cells.
  5. type II PtdIns 4-kinase beta is a key component in early T cell activation signaling cascades
    Title: Type II phosphatidylinositol 4-kinase β is an integral signaling component of early T cell activation mechanisms.
  6. PIP4Kbeta interacts with and modulates nuclear localization of the PIP4Kalpha.
    Title: PIP4Kbeta interacts with and modulates nuclear localization of the high-activity PtdIns5P-4-kinase isoform PIP4Kalpha.
  7. There is no evidence to suggest that PI4K2B is contributing to bipolar disorder in this family but a role for this gene in schizophrenia has not been excluded.
    Title: A case-control association study and family-based expression analysis of the bipolar disorder candidate gene PI4K2B.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: A case-control association study and family-based expression analysis of the bipolar disorder candidate gene PI4K2B.
  9. LB-PI4K2B-1S-specific CD4(+) T cells contributed to the antitumor response by both directly eliminating malignant cells as effector cells and stimulating CD8(+) T cell immunity as helper cells.
    Title: Identification of phosphatidylinositol 4-kinase type II beta as HLA class II-restricted target in graft versus leukemia reactivity.
  10. Type II PtdIns 4-kinase beta interacts with TCR-CD3 zeta chain. The C-terminal ITAM is critical for enzyme docking on the zeta chain. The association is tyrosyl phosphorylation dependent. Mutation of Y-151 & Y-142 disrupts interaction of the 2 proteins.
    Title: Type II phosphatidylinositol 4-kinase beta associates with TCR-CD3 zeta chain in Jurkat cells.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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

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

  • FLJ11105

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 1-phosphatidylinositol 4-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 1-phosphatidylinositol 4-kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 1-phosphatidylinositol 4-kinase activity TAS
Traceable Author Statement
more info
  
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Golgi organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosome organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in phosphatidylinositol phosphate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylinositol phosphate biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in early endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane HDA 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 
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
phosphatidylinositol 4-kinase type 2-beta
Names
PI4KII-BETA
phosphatidylinositol 4-kinase type-II beta
NP_060793.2
XP_005248231.1
XP_005248232.1
XP_054206387.1
XP_054206388.1

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_052594.1 RefSeqGene

    Range
    5003..50174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018323.4 → NP_060793.2  phosphatidylinositol 4-kinase type 2-beta

    See identical proteins and their annotated locations for NP_060793.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AC108218, AY091514, BC051749
    Consensus CDS
    CCDS3433.1
    UniProtKB/Swiss-Prot
    Q8TCG2, Q9NUW2
    UniProtKB/TrEMBL
    B3KY39
    Related
    ENSP00000264864.6, ENST00000264864.8
    Conserved Domains (1) summary
    pfam00454
    Location:130 → 427
    PI3_PI4_kinase; Phosphatidylinositol 3- and 4-kinase

RNA

  1. NR_144633.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site at an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC104662, AC108218

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    25234033..25279204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248174.3 → XP_005248231.1  phosphatidylinositol 4-kinase type 2-beta isoform X1

    UniProtKB/TrEMBL
    B3KY39
    Conserved Domains (1) summary
    pfam00454
    Location:130 → 422
    PI3_PI4_kinase; Phosphatidylinositol 3- and 4-kinase

  2. XM_005248175.5 → XP_005248232.1  phosphatidylinositol 4-kinase type 2-beta isoform X2

    See identical proteins and their annotated locations for XP_005248232.1

    UniProtKB/TrEMBL
    B4DJZ0, G5E9Z4
    Related
    ENSP00000423373.1, ENST00000512921.4
    Conserved Domains (1) summary
    pfam00454
    Location:34 → 331
    PI3_PI4_kinase; Phosphatidylinositol 3- and 4-kinase

RNA

  1. XR_007057941.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    25215954..25261023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350412.1 → XP_054206387.1  phosphatidylinositol 4-kinase type 2-beta isoform X1

    UniProtKB/TrEMBL
    B3KY39

  2. XM_054350413.1 → XP_054206388.1  phosphatidylinositol 4-kinase type 2-beta isoform X2

    UniProtKB/TrEMBL
    B4DJZ0, G5E9Z4

RNA

  1. XR_008487014.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TCG2.1 GenPept UniProtKB/Swiss-Prot:Q8TCG2

Gene LinkOut

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