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

    Gene ID: 79837, updated on 3-Nov-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 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process; negative regulation of insulin receptor signaling pathway; and positive regulation of autophagosome assembly. Located in several cellular components, including autophagosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 18.0), kidney (RPKM 16.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PIP4K2C in Genome Data Viewer
    Location:
    12q13.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57591192..57603418)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57559429..57571638)
    RS_2024_09 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 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. Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Rogava M, et al. Nat Cancer, 2024 Mar. PMID 38286827, Free PMC Article
    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. Zhang Y, et al. Hepatology, 2021 Feb. PMID 32374916
    3. 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
    4. 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
    5. A new pathway for synthesis of phosphatidylinositol-4,5-bisphosphate. Rameh LE, et al. Nature, 1997 Nov 13. PMID 9367159

    See all (77) 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 membrane-bounded 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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    NEW Try the new Transcript table

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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