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

Summary

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

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_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of lysosomal positioning via TMEM55B phosphorylation.
Title: Regulation of lysosomal positioning via TMEM55B phosphorylation.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2636 (e-PCR)
- UniSTS:70413

WI-18729 (e-PCR)
- UniSTS:63042

SHGC-36712 (e-PCR)
- UniSTS:60513

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

EC 3.1.3.78

NP_653169.2

EC 3.1.3.78

XP_024305507.1

EC 3.1.3.78

XP_024305508.1

EC 3.1.3.78

XP_054189126.1

EC 3.1.3.78

XP_054189127.1

EC 3.1.3.78

XP_054232918.1

EC 3.1.3.78

XP_054232919.1

EC 3.1.3.78

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)

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
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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

20457681..20461434 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Reference GRCh38.p14 PATCHES

Genomic

NW_025791796.1 Reference GRCh38.p14 PATCHES

Range

660362..664115 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054333152.1 → XP_054189127.1 type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X2
XM_054333151.1 → XP_054189126.1 type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

14654584..14658337 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054376944.1 → XP_054232919.1 type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X2
XM_054376943.1 → XP_054232918.1 type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase isoform X1