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PIP5K1C phosphatidylinositol-4-phosphate 5-kinase type 1 gamma [ Homo sapiens (human) ]

Gene ID: 23396, updated on 3-Apr-2024

Summary

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Official Symbol
PIP5K1Cprovided by HGNC
Official Full Name
phosphatidylinositol-4-phosphate 5-kinase type 1 gammaprovided by HGNC
Primary source
HGNC:HGNC:8996
See related
Ensembl:ENSG00000186111 MIM:606102; AllianceGenome:HGNC:8996
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
LCCS3; PIP5Kgamma; PIP5K-GAMMA; PIP5K1-gamma
Summary
This locus encodes a type I phosphatidylinositol 4-phosphate 5-kinase. The encoded protein catalyzes phosphorylation of phosphatidylinositol 4-phosphate, producing phosphatidylinositol 4,5-bisphosphate. This enzyme is found at synapses and has been found to play roles in endocytosis and cell migration. Mutations at this locus have been associated with lethal congenital contractural syndrome. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Sep 2010]
Expression
Broad expression in testis (RPKM 14.7), brain (RPKM 13.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.3
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3630183..3700468, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3608310..3678870, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3630181..3700466, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3605850-3606424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3606998-3607571 Neighboring gene thromboxane A2 receptor Neighboring gene CACTIN antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3618043-3618915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3623949-3624450 Neighboring gene cactin, spliceosome C complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3624451-3624950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3625177-3625738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3625739-3626300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:3626301-3626862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3643569-3644108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3644109-3644646 Neighboring gene MPRA-validated peak3250 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3665265-3666095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3672153-3672828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3673765-3674558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3675389-3675890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3679833-3680333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3681521-3682070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682071-3682618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682619-3683168 Neighboring gene Sharpr-MPRA regulatory region 323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13743 Neighboring gene Sharpr-MPRA regulatory region 5698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3699523-3700306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3707827-3708490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3708491-3709152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3709988-3710533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3712547-3713048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3713049-3713548 Neighboring gene tight junction protein 3 Neighboring gene MPRA-validated peak3252 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3761575-3761892 Neighboring gene uncharacterized LOC105372248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13744 Neighboring gene amyloid beta precursor protein binding family A member 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. PIPKIγ Regulates CCL2 Expression in Colorectal Cancer by Activating AKT-STAT3 Signaling. Xue J, et al. J Immunol Res, 2019. PMID 31781676, Free PMC Article
  2. Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer. Peng W, et al. EBioMedicine, 2019 Jun. PMID 31105034, Free PMC Article
  3. Cdk5-mediated phosphorylation regulates phosphatidylinositol 4-phosphate 5-kinase type I γ 90 activity and cell invasion. Li L, et al. FASEB J, 2019 Jan. PMID 30040488, Free PMC Article
  4. Silencing of type Iγ phosphatidylinositol phosphate kinase suppresses ovarian cancer cell proliferation, migration and invasion. Cao S, et al. Oncol Rep, 2017 Jul. PMID 28560454, Free PMC Article
  5. PIPKIγ targets to the centrosome and restrains centriole duplication. Xu Q, et al. J Cell Sci, 2014 Mar 15. PMID 24434581, Free PMC Article

See all (81) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis.
    Title: CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis.
  2. Type I Phosphatidylinositol-4-Phosphate 5-Kinases alpha and gamma Play a Key Role in Targeting HIV-1 Pr55(Gag) to the Plasma Membrane.
    Title: Type I Phosphatidylinositol-4-Phosphate 5-Kinases α and γ Play a Key Role in Targeting HIV-1 Pr55(Gag) to the Plasma Membrane.
  3. our observations revealed that high PIPKIgamma expression in tumor cells could induce AKT-mTOR signaling activation. Increased activation of AKT-mTOR increases the phosphorylation levels of STAT3, leading to CCL2 expression and suppressing cancer immune reaction activation.
    Title: PIPKIγ Regulates CCL2 Expression in Colorectal Cancer by Activating AKT-STAT3 Signaling.
  4. Our findings reveal a new regulatory role of PIPKIgamma in Warburg effect and provide a key contributor in colorectal cancer metabolism with potential therapeutic potentials.
    Title: Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer.
  5. PIP5K1C was significantly associated with Alcohol Use Disorder in the African ancestry group. However, a replication analysis using an independent sample (N = 3,801) found no significant associations after correction for multiple testing.
    Title: Genetic Association and Expression Analyses of the Phosphatidylinositol-4-Phosphate 5-Kinase (PIP5K1C) Gene in Alcohol Use Disorder-Relevance for Pain Signaling and Alcohol Use.
  6. Cdk5-mediated PIPKIgamma90 phosphorylation is essential for cell invasion leading to breast cancer.
    Title: Cdk5-mediated phosphorylation regulates phosphatidylinositol 4-phosphate 5-kinase type I γ 90 activity and cell invasion.
  7. The Btk-dependent PIP5K1gamma lipid kinase activation by Fas counteracts FasL-induced cell death.
    Title: The Btk-dependent PIP5K1γ lipid kinase activation by Fas counteracts FasL-induced cell death.
  8. High expression of PIP5K1-gamma is associated with colorectal cancer.
    Title: Silencing of type Iγ phosphatidylinositol phosphate kinase suppresses ovarian cancer cell proliferation, migration and invasion.
  9. These data reveal a novel function for PKD1 as a regulator of focal adhesion dynamics and by identifying PIP5Klgamma as a novel PKD1 substrate provide mechanistic insight into this process.
    Title: Protein Kinase D1 regulates focal adhesion dynamics and cell adhesion through Phosphatidylinositol-4-phosphate 5-kinase type-l γ.
  10. PIPKIgamma promotes the transcription of the PD-L1 gene by activating the NF-kappaB pathway in these cells. These results demonstrate that PIPKIgamma-dependent expression of PD-L1 is likely important for the progression of triple negative breast cancer.
    Title: Type Iγ phosphatidylinositol phosphate kinase regulates PD-L1 expression by activating NF-κB.
Submit: New GeneRIF Correction See all GeneRIFs (40)

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

Associated conditions

Description Tests
Lethal congenital contracture syndrome 3
MedGen: C1969655 OMIM: 611369 GeneReviews: Not available
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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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of phosphatidylinositol-4-phosphate 5-kinase, type I, gamma (PIP5K1C) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

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

  • KIAA0589

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 TAS
Traceable Author Statement
more info
  
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol kinase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization TAS
Traceable Author Statement
more info
 PubMed 
involved_in adherens junction assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell-cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in clathrin-dependent endocytosis TAS
Traceable Author Statement
more info
 PubMed 
involved_in membrane organization TAS
Traceable Author Statement
more info
  
involved_in neutrophil chemotaxis TAS
Traceable Author Statement
more info
 PubMed 
involved_in phagocytosis TAS
Traceable Author Statement
more info
 PubMed 
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 phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction TAS
Traceable Author Statement
more info
  
involved_in synaptic vesicle endocytosis TAS
Traceable Author Statement
more info
 PubMed 
involved_in synaptic vesicle exocytosis TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in adherens junction IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in focal adhesion TAS
Traceable Author Statement
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in phagocytic cup IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in ruffle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in uropod TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
Names
PIP5K1gamma
diphosphoinositide kinase
phosphatidylinositol-4-phosphate 5-kinase, type I, gamma
ptdIns(4)P-5-kinase 1 gamma
type I PIP kinase
type I phosphatidylinositol 4-phosphate 5-kinase gamma
NP_001182662.1
NP_001287778.1
NP_036530.1
XP_011526150.1
XP_011526151.1
XP_016882029.1
XP_047294489.1
XP_047294490.1
XP_047294491.1
XP_047294492.1
XP_047294493.1
XP_054176363.1
XP_054176364.1
XP_054176365.1
XP_054176366.1
XP_054176367.1
XP_054176368.1
XP_054176369.1
XP_054176370.1

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_012161.2 RefSeqGene

    Range
    4980..75265
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195733.2 → NP_001182662.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1, also known as PIPKIgamma640 and PIPKIgamma87).
    Source sequence(s)
    AB011161, AK315912, BC011138, DC389567
    Consensus CDS
    CCDS56074.1
    UniProtKB/TrEMBL
    B4DVZ9
    Related
    ENSP00000445992.1, ENST00000539785.5
    Conserved Domains (1) summary
    cd17308
    Location:76 → 449
    PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

  2. NM_001300849.2 → NP_001287778.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 3

    See identical proteins and their annotated locations for NP_001287778.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as PIPKIgamma_v5) encodes the longest isoform (3, also known as PIPKIgamma_i5).
    Source sequence(s)
    FJ965537, HY000479
    Consensus CDS
    CCDS74257.1
    UniProtKB/TrEMBL
    B4DVZ9
    Related
    ENSP00000466363.1, ENST00000589578.5
    Conserved Domains (2) summary
    PHA03151
    Location:497 → 672
    PHA03151; hypothetical protein; Provisional
    smart00330
    Location:103 → 443
    PIPKc; Phosphatidylinositol phosphate kinases

  3. NM_012398.3 → NP_036530.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 2

    See identical proteins and their annotated locations for NP_036530.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate, in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2, also known as PIPKIgamma668 and PIPKIgamma90) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB011161, AK315912, BC011138, DC389567
    Consensus CDS
    CCDS32872.1
    UniProtKB/Swiss-Prot
    B7Z9E7, C6GIJ7, C6GIJ8, O60331, Q7LE07
    UniProtKB/TrEMBL
    B4DVZ9
    Related
    ENSP00000335333.3, ENST00000335312.8
    Conserved Domains (1) summary
    cd17308
    Location:76 → 449
    PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3630183..3700468 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438535.1 → XP_047294491.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X6

  2. XM_017026540.3 → XP_016882029.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X4

    UniProtKB/TrEMBL
    B4DVZ9

  3. XM_011527849.2 → XP_011526151.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X5

    UniProtKB/TrEMBL
    B4DVZ9
    Conserved Domains (1) summary
    smart00330
    Location:103 → 443
    PIPKc; Phosphatidylinositol phosphate kinases

  4. XM_011527848.2 → XP_011526150.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X3

    UniProtKB/TrEMBL
    B4DVZ9
    Conserved Domains (2) summary
    PHA03151
    Location:497 → 665
    PHA03151; hypothetical protein; Provisional
    cd17308
    Location:76 → 449
    PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

  5. XM_047438533.1 → XP_047294489.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X1

    Related
    ENSP00000444779.1, ENST00000537021.1

  6. XM_047438534.1 → XP_047294490.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X2

  7. XM_047438536.1 → XP_047294492.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X7

  8. XM_047438537.1 → XP_047294493.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3608310..3678870 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320393.1 → XP_054176368.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X6

  2. XM_054320391.1 → XP_054176366.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X4

  3. XM_054320392.1 → XP_054176367.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X5

  4. XM_054320390.1 → XP_054176365.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X3

  5. XM_054320388.1 → XP_054176363.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X1

  6. XM_054320389.1 → XP_054176364.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X2

  7. XM_054320394.1 → XP_054176369.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X7

  8. XM_054320395.1 → XP_054176370.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60331.2 GenPept UniProtKB/Swiss-Prot:O60331

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