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

Summary

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: mouse all
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Genomic context

Location:: 4p15.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (25234033..25279204)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (25215954..25261023)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (25235655..25280826)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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
involved_in phosphorylation	IEA Inferred from Electronic Annotation more info

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 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
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

EC 2.7.1.67

XP_005248231.1

EC 2.7.1.67

XP_005248232.1

EC 2.7.1.67

XP_054206387.1

EC 2.7.1.67

XP_054206388.1

EC 2.7.1.67

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

NG_052594.1 RefSeqGene

Range

5003..50174

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

25234033..25279204

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

XR_007057941.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

25215954..25261023

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054350412.1 → XP_054206387.1 phosphatidylinositol 4-kinase type 2-beta isoform X1
XM_054350413.1 → XP_054206388.1 phosphatidylinositol 4-kinase type 2-beta isoform X2

UniProtKB/TrEMBL

G5E9Z4