PIP4K2A phosphatidylinositol-5-phosphate 4-kinase type 2 alpha [Homo sapiens (human)] - Gene

Summary

Official Symbol: PIP4K2Aprovided by HGNC
Official Full Name: phosphatidylinositol-5-phosphate 4-kinase type 2 alphaprovided by HGNC
Primary source: HGNC:HGNC:8997
See related: Ensembl:ENSG00000150867 MIM:603140; AllianceGenome:HGNC:8997
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: PIPK; PI5P4KA; PIP5K2A; PIP5KIIA; PIP5KII-alpha
Summary: Phosphatidylinositol-5,4-bisphosphate, the precursor to second messengers of the phosphoinositide signal transduction pathways, is thought to be involved in the regulation of secretion, cell proliferation, differentiation, and motility. The protein encoded by this gene is one of a family of enzymes capable of catalyzing the phosphorylation of phosphatidylinositol-5-phosphate on the fourth hydroxyl of the myo-inositol ring to form phosphatidylinositol-5,4-bisphosphate. The amino acid sequence of this enzyme does not show homology to other kinases, but the recombinant protein does exhibit kinase activity. This gene is a member of the phosphatidylinositol-5-phosphate 4-kinase family. [provided by RefSeq, Jul 2008]
Expression: Broad expression in brain (RPKM 41.4), lymph node (RPKM 29.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10p12.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (22534854..22714578, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (22553890..22733579, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (22823783..23003507, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Metabolic Enzyme SLC27A5 Regulates PIP4K2A pre-mRNA Splicing as a Noncanonical Mechanism to Suppress Hepatocellular Carcinoma Metastasis.
Title: Metabolic Enzyme SLC27A5 Regulates PIP4K2A pre-mRNA Splicing as a Noncanonical Mechanism to Suppress Hepatocellular Carcinoma Metastasis.
Contributions of ARID5B, IKZF1, PIP4K2A, and GATA3 Gene Polymorphisms to Childhood Acute Lymphoblastic Leukemia in a Chinese Population.
Title: Contributions of ARID5B, IKZF1, PIP4K2A, and GATA3 Gene Polymorphisms to Childhood Acute Lymphoblastic Leukemia in a Chinese Population.
Association of PIP4K2A Polymorphisms with Alcohol Use Disorder.
Title: Association of PIP4K2A Polymorphisms with Alcohol Use Disorder.
Distribution and localization of phosphatidylinositol 5-phosphate, 4-kinase alpha and beta in the brain.
Title: Distribution and localization of phosphatidylinositol 5-phosphate, 4-kinase alpha and beta in the brain.
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.
PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay.
Title: PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay.
Thermal proteome profiling identifies PIP4K2A and ZADH2 as off-targets of Polo-like kinase 1 inhibitor volasertib.
Title: Thermal proteome profiling identifies PIP4K2A and ZADH2 as off-targets of Polo-like kinase 1 inhibitor volasertib.
Discovery and Differential Processing of HLA Class II-Restricted Minor Histocompatibility Antigen LB-PIP4K2A-1S and Its Allelic Variant by Asparagine Endopeptidase.
Title: Discovery and Differential Processing of HLA Class II-Restricted Minor Histocompatibility Antigen LB-PIP4K2A-1S and Its Allelic Variant by Asparagine Endopeptidase.
Genetic polymorphisms of PIP5K2A and course of schizophrenia.
Title: Genetic polymorphisms of PIP5K2A and course of schizophrenia.
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.

Submit: New GeneRIF Correction See all GeneRIFs (44)

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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Markers

D10S553 (e-PCR)
- UniSTS:4879

RH46424 (e-PCR)
- UniSTS:89887

D10S553 (e-PCR)
- UniSTS:32035

RH78590 (e-PCR)
- UniSTS:15442

SHGC-58154 (e-PCR)
- UniSTS:4698

D10S1259 (e-PCR)
- UniSTS:47966

D10S1522 (e-PCR)
- UniSTS:153723

WIAF-1715 (e-PCR)
- UniSTS:2432

SHGC-84121 (e-PCR)
- UniSTS:104576

D10S1568 (e-PCR)
- UniSTS:13703

D10S2371 (e-PCR)
- UniSTS:43403

SHGC-54644 (e-PCR)
- UniSTS:49803

G63324 (e-PCR)
- UniSTS:140437

A006T43 (e-PCR)
- UniSTS:11690

SHGC-132136 (e-PCR)
- UniSTS:170667

RH70570 (e-PCR)
- UniSTS:72882

D10S1662 (e-PCR), detects polymorphism
- UniSTS:79293

D10S1621E (e-PCR)
- UniSTS:154070

STS-H93068 (e-PCR)
- UniSTS:72924

SHGC-33797 (e-PCR)
- UniSTS:69371

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-4-phosphate 5-kinase activity	NAS Non-traceable Author Statement more info	PubMed
enables 1-phosphatidylinositol-5-phosphate 4-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 1-phosphatidylinositol-5-phosphate 4-kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
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 megakaryocyte development	IEA Inferred from Electronic Annotation more info
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
involved_in vesicle-mediated cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in autophagosome	IMP Inferred from Mutant Phenotype 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 lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
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 alpha

Names: 1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha; 1-phosphatidylinositol-4-phosphate kinase; 1-phosphatidylinositol-4-phosphate-5-kinase; PI(5)P 4-kinase type II alpha; PI5P4Kalpha; PIP4KII-alpha; PIP5KIII; PIP5KIIalpha; diphosphoinositide kinase 2-alpha; phosphatidylinositol 5-phosphate 4-kinase type II alpha; phosphatidylinositol-4-phosphate 5-kinase, type II, alpha

NP_001316991.1

EC 2.7.1.149

NP_005019.2

EC 2.7.1.149

XP_006717513.1

EC 2.7.1.149

XP_016871819.1

EC 2.7.1.149

XP_016871820.1

EC 2.7.1.149

XP_047281307.1

EC 2.7.1.149

XP_054222063.1

EC 2.7.1.149

XP_054222064.1

EC 2.7.1.149

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)

NM_001330062.2 → NP_001316991.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate 5'-terminal exon resulting in a different 5' UTR and use of a downstream AUG compared to variant 1. It encodes isoform 2, which has a shorter N-terminus than isoform 1.

Source sequence(s)

AK294817, AL513128

Consensus CDS

CCDS81443.1

UniProtKB/Swiss-Prot

P48426

Related

ENSP00000442098.1, ENST00000545335.5

Conserved Domains (1) summary

cl28923
Location:1 → 344

PIPKc; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family
NM_005028.5 → NP_005019.2 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform 1

See identical proteins and their annotated locations for NP_005019.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL390318, AL513128, BC018034, DB504104

Consensus CDS

CCDS7141.1

UniProtKB/Swiss-Prot

B0YJ66, B4DGX2, D3DRV1, P48426, P53807, Q5VUX3

Related

ENSP00000365757.4, ENST00000376573.9

Conserved Domains (1) summary

cd17309
Location:27 → 403

PIPKc_PIP5K2A; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (PIP5K2A) 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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

22534854..22714578 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006717450.3 → XP_006717513.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X1

See identical proteins and their annotated locations for XP_006717513.1

Conserved Domains (1) summary

cl28923
Location:27 → 352

PIPKc; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family
XM_017016330.2 → XP_016871819.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X2

UniProtKB/Swiss-Prot

P48426

Conserved Domains (1) summary

cl28923
Location:1 → 344

PIPKc; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family
XM_047425351.1 → XP_047281307.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X2
XM_017016331.2 → XP_016871820.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X2

UniProtKB/Swiss-Prot

P48426

Conserved Domains (1) summary

cl28923
Location:1 → 344

PIPKc; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

22553890..22733579 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054366088.1 → XP_054222063.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X1
XM_054366089.1 → XP_054222064.1 phosphatidylinositol 5-phosphate 4-kinase type-2 alpha isoform X2