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PIP4K2C phosphatidylinositol-5-phosphate 4-kinase type 2 gamma [ Homo sapiens (human) ]

Gene ID: 79837, updated on 3-Apr-2024

Summary

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Official Symbol
PIP4K2Cprovided by HGNC
Official Full Name
phosphatidylinositol-5-phosphate 4-kinase type 2 gammaprovided by HGNC
Primary source
HGNC:HGNC:23786
See related
Ensembl:ENSG00000166908 MIM:617104; AllianceGenome:HGNC:23786
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PIP5K2C
Summary
Enables 1-phosphatidylinositol-4-phosphate 5-kinase activity and identical protein binding activity. Involved in several processes, including 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process; negative regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity; and positive regulation of autophagosome assembly. Located in several cellular components, including autophagosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 18.0), kidney (RPKM 16.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57591192..57603418)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57559429..57571638)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57984975..57997201)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methyl-CpG binding domain protein 6 Neighboring gene dynactin subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57944162-57944754 Neighboring gene kinesin family member 5A Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57955995-57956161 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57956855-57957072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6549 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:57984713-57985214 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57997977-57998488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57998489-57999001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4586 Neighboring gene Rho guanine nucleotide exchange factor 25 Neighboring gene deltex E3 ubiquitin ligase 3

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. C24-Ceramide Drives Gallbladder Cancer Progression Through Directly Targeting Phosphatidylinositol 5-Phosphate 4-Kinase Type-2 Gamma to Facilitate Mammalian Target of Rapamycin Signaling Activation. Zhang Y, et al. Hepatology, 2021 Feb. PMID 32374916
  2. PIP4K2A and PIP4K2C transcript levels are associated with cytogenetic risk and survival outcomes in acute myeloid leukemia. Lima K, et al. Cancer Genet, 2019 Apr. PMID 31109595
  3. The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis. Sumita K, et al. Mol Cell, 2016 Jan 21. PMID 26774281, Free PMC Article
  4. PIP4Ks Suppress Insulin Signaling through a Catalytic-Independent Mechanism. Wang DG, et al. Cell Rep, 2019 May 14. PMID 31091439, Free PMC Article
  5. Functional analysis of the biochemical activity of mammalian phosphatidylinositol 5 phosphate 4-kinase enzymes. Mathre S, et al. Biosci Rep, 2019 Feb 28. PMID 30718367, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.
    Title: Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.
  2. C24-Ceramide Drives Gallbladder Cancer Progression Through Directly Targeting Phosphatidylinositol 5-Phosphate 4-Kinase Type-2 Gamma to Facilitate Mammalian Target of Rapamycin Signaling Activation.
    Title: C24-Ceramide Drives Gallbladder Cancer Progression Through Directly Targeting Phosphatidylinositol 5-Phosphate 4-Kinase Type-2 Gamma to Facilitate Mammalian Target of Rapamycin Signaling Activation.
  3. 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.
  4. study provides additional evidence of the involvement of members of the PIP4K2 family, in particular PIP4K2A and PIP4K2C, in AML
    Title: PIP4K2A and PIP4K2C transcript levels are associated with cytogenetic risk and survival outcomes in acute myeloid leukemia.
  5. Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
    Title: Genetic variants in the prediction of rheumatoid arthritis.
  6. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of a single-nucleotide polymorphism in CD40 with the rate of joint destruction in rheumatoid arthritis.
Submit: New GeneRIF Correction

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
Common variants at CD40 and other loci confer risk of rheumatoid arthritis.
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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Homology

Clone Names

  • FLJ22055

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 IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
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 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 
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
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in intracellular organelle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
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
  

General protein information

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Preferred Names
phosphatidylinositol 5-phosphate 4-kinase type-2 gamma
Names
PI(5)P 4-kinase type II gamma
PIP4KII-gamma
phosphatidylinositol 4-phosphate 5-kinase
phosphatidylinositol 5-phosphate 4-kinase type II gamma
phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
NP_001139730.1
NP_001139731.1
NP_001139732.1
NP_079055.3
XP_005269209.1
XP_011537049.1
XP_047285507.1
XP_047285508.1
XP_054229219.1
XP_054229220.1
XP_054229221.1
XP_054229222.1

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_001146258.2 → NP_001139730.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform a

    See identical proteins and their annotated locations for NP_001139730.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AC022506, KF459552
    Consensus CDS
    CCDS8946.1
    UniProtKB/Swiss-Prot
    B2RDL3, B4DM11, B4DY44, Q8TBX8, Q9H6N2
    UniProtKB/TrEMBL
    B3KWP7
    Related
    ENSP00000439878.2, ENST00000540759.6
    Conserved Domains (1) summary
    smart00330
    Location:72 → 420
    PIPKc; Phosphatidylinositol phosphate kinases

  2. NM_001146259.2 → NP_001139731.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform b

    See identical proteins and their annotated locations for NP_001139731.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses two alternate in-frame splice sites in the 5' coding region compared to variant 1. This results in a shorter protein (isoform b) compared to isoform a.
    Source sequence(s)
    AC022506, KF459552
    Consensus CDS
    CCDS55839.1
    UniProtKB/TrEMBL
    B3KWP7
    Related
    ENSP00000447390.1, ENST00000550465.5
    Conserved Domains (1) summary
    smart00330
    Location:72 → 402
    PIPKc; Phosphatidylinositol phosphate kinases

  3. NM_001146260.2 → NP_001139732.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform c

    See identical proteins and their annotated locations for NP_001139732.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region codon compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC022506, KF459552
    Consensus CDS
    CCDS53808.1
    UniProtKB/TrEMBL
    B3KWP7
    Related
    ENSP00000412035.3, ENST00000422156.7
    Conserved Domains (1) summary
    smart00330
    Location:72 → 372
    PIPKc; Phosphatidylinositol phosphate kinases

  4. NM_024779.5 → NP_079055.3  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform a

    See identical proteins and their annotated locations for NP_079055.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AC022506, KF459552
    Consensus CDS
    CCDS8946.1
    UniProtKB/Swiss-Prot
    B2RDL3, B4DM11, B4DY44, Q8TBX8, Q9H6N2
    UniProtKB/TrEMBL
    B3KWP7
    Related
    ENSP00000347032.5, ENST00000354947.10
    Conserved Domains (1) summary
    smart00330
    Location:72 → 420
    PIPKc; Phosphatidylinositol phosphate kinases

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57591192..57603418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269152.4 → XP_005269209.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X1

    UniProtKB/TrEMBL
    B3KWP7
    Conserved Domains (1) summary
    smart00330
    Location:72 → 407
    PIPKc; Phosphatidylinositol phosphate kinases

  2. XM_011538747.3 → XP_011537049.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X4

    UniProtKB/TrEMBL
    B3KQV3, E7ERY6
    Conserved Domains (1) summary
    cl02572
    Location:45 → 230
    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_047429551.1 → XP_047285507.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X2

  4. XM_047429552.1 → XP_047285508.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57559429..57571638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373244.1 → XP_054229219.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X1

  2. XM_054373247.1 → XP_054229222.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X4

  3. XM_054373245.1 → XP_054229220.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X2

  4. XM_054373246.1 → XP_054229221.1  phosphatidylinositol 5-phosphate 4-kinase type-2 gamma isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TBX8.3 GenPept UniProtKB/Swiss-Prot:Q8TBX8

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