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

Gene ID: 90809, updated on 5-Mar-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
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Genomic context

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Location:
14q11.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (20457681..20461434, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (14654584..14658337, complement)
105.20220307 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
  • 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. Regulation of lysosomal positioning via TMEM55B phosphorylation. Araki M, et al. J Biochem, 2021 Jul 3. PMID 33537719
  2. 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
  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 (40) 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_2023_10

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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