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    PIP4P1 phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1 [ Homo sapiens (human) ]

    Gene ID: 90809, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PIP4P1provided by HGNC
    Official Full Name
    phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1provided by HGNC
    Primary source
    HGNC:HGNC:19299
    See related
    Ensembl:ENSG00000165782 MIM:609865; AllianceGenome:HGNC:19299
    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
    C14orf9; TMEM55B
    Summary
    TMEM55B catalyzes the degradation of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2) by removing the 4-phosphate (Ungewickell et al., 2005 [PubMed 16365287]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 22.8), thyroid (RPKM 17.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PIP4P1 in Genome Data Viewer
    Location:
    14q11.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (20457681..20461434, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (14654584..14658337, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (20925840..20929593, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene solute carrier family 12 member 3 pseudogene Neighboring gene OSGEP/APEX1 bi-directional promoter region Neighboring gene O-sialoglycoprotein endopeptidase Neighboring gene Sharpr-MPRA regulatory region 9617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:20928913-20929879 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:20929880-20930845 Neighboring gene apurinic/apyrimidinic endodeoxyribonuclease 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:20937332-20937836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8079 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:20945841-20946029 Neighboring gene purine nucleoside phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8080 Neighboring gene ribonuclease A family member 10 (inactive)

    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. Type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase regulates stress-induced apoptosis. Zou J, et al. Proc Natl Acad Sci U S A, 2007 Oct 23. PMID 17940011, Free PMC Article
    2. Regulation of lysosomal positioning via TMEM55B phosphorylation. Araki M, et al. J Biochem, 2021 Jul 3. PMID 33537719
    3. Transmembrane protein 55B is a novel regulator of cellular cholesterol metabolism. Medina MW, et al. Arterioscler Thromb Vasc Biol, 2014 Sep. PMID 25035345, Free PMC Article
    4. The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases. Ungewickell A, et al. Proc Natl Acad Sci U S A, 2005 Dec 27. PMID 16365287, Free PMC Article
    5. TMEM55B contributes to lysosomal homeostasis and amino acid-induced mTORC1 activation. Hashimoto Y, et al. Genes Cells, 2018 Jun. PMID 29644770

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Regulation of lysosomal positioning via TMEM55B phosphorylation.
      Title: Regulation of lysosomal positioning via TMEM55B phosphorylation.
    2. Results suggest that TMEM55B contributes to assembly of the V-ATPase complex in lipid rafts of the lysosomal membrane and to subsequent activation of mTORC1.
      Title: TMEM55B contributes to lysosomal homeostasis and amino acid-induced mTORC1 activation.
    3. these data suggest that the TFEB/TMEM55B/JIP4 pathway coordinates lysosome movement in response to a variety of stress conditions.
      Title: TFEB regulates lysosomal positioning by modulating TMEM55B expression and JIP4 recruitment to lysosomes.
    4. Expression array profiling was performed on lymphoblastoid cell lines from statin clinical trial participants showed sterol-regulated expression of TMEM55B. Knockdown promoted LDL receptor decay and decreased its cholesterol uptake.
      Title: Transmembrane protein 55B is a novel regulator of cellular cholesterol metabolism.
    5. Type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase (type I 4-phosphatase), an enzyme that dephosphorylates phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P(2)), forming PtdIns-5-P in vitro, can increase the cellular levels of PtdIns-5-P.
      Title: Type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase regulates stress-induced apoptosis.
    6. identification and characterization of two previously undescribed human enzymes, PtdIns-4,5-P(2) 4-phosphatase type I and type II
      Title: The identification and characterization of two phosphatidylinositol-4,5-bisphosphate 4-phosphatases.
    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
    Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with transmembrane protein 55B (TMEM55B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

    • MGC26684, DKFZp434M0519

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lysosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phosphatidylinositol dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phospholipid metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in positive regulation of TORC1 signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proton-transporting V-type ATPase complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of signal transduction by p53 class mediator TAS
    Traceable Author Statement
    more info
    		  
    involved_in response to sterol depletion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in phagocytic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagocytic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
    Names
    ptdIns-4,5-P(2) 4-phosphatase type I
    ptdIns-4,5-P2 4-Ptase I
    transmembrane protein 55B
    type 1 PtdIns-4,5-P2 4-Ptase
    type I PtdIns-4,5-P(2) 4-phosphatase
    type I phosphatidylinositol-4,5-bisphosphate 4-phosphatase
    NP_001094284.1
    NP_653169.2
    XP_024305507.1
    XP_024305508.1
    XP_054189126.1
    XP_054189127.1
    XP_054232918.1
    XP_054232919.1

    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_001100814.3 → NP_001094284.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform 1

      See identical proteins and their annotated locations for NP_001094284.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK314021, AL355075, BX161490, BX248025, CA430067
      Consensus CDS
      CCDS41911.1
      UniProtKB/Swiss-Prot
      Q86T03
      Related
      ENSP00000381102.4, ENST00000398020.6
      Conserved Domains (1) summary
      pfam09788
      Location:4 → 277
      Tmemb_55A; Transmembrane protein 55A

    2. NM_144568.4 → NP_653169.2  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform 2

      See identical proteins and their annotated locations for NP_653169.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK314021, AL355075, BX161490, CA430067
      Consensus CDS
      CCDS9551.1
      UniProtKB/Swiss-Prot
      B2RA35, Q86T03, Q86U09, Q8WUC0, Q9BU67, Q9NSU8
      Related
      ENSP00000250489.4, ENST00000250489.9
      Conserved Domains (1) summary
      pfam09788
      Location:4 → 270
      Tmemb_55A; Transmembrane protein 55A

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      20457681..20461434 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024449740.2 → XP_024305508.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X2

      Conserved Domains (1) summary
      pfam09788
      Location:4 → 147
      Tmemb_55A; Transmembrane protein 55A

    2. XM_024449739.2 → XP_024305507.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X1

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791796.1 Reference GRCh38.p14 PATCHES

      Range
      660362..664115 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333152.1 → XP_054189127.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X2

    2. XM_054333151.1 → XP_054189126.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      14654584..14658337 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376944.1 → XP_054232919.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X2

    2. XM_054376943.1 → XP_054232918.1  type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86T03.1 GenPept UniProtKB/Swiss-Prot:Q86T03

    Gene LinkOut

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

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