PLEKHF2 pleckstrin homology and FYVE domain containing 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLEKHF2provided by HGNC
Official Full Name: pleckstrin homology and FYVE domain containing 2provided by HGNC
Primary source: HGNC:HGNC:20757
See related: Ensembl:ENSG00000175895 MIM:615208; AllianceGenome:HGNC:20757
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: EAPF; PHAFIN2; ZFYVE18
Summary: Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in endosome organization and endosome to lysosome transport. Located in transport vesicle. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in bone marrow (RPKM 31.1), lymph node (RPKM 29.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q22.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (95133785..95156685)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (96259034..96281932)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (96146013..96168913)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The phosphoinositide coincidence detector Phafin2 promotes macropinocytosis by coordinating actin organisation at forming macropinosomes.
Title: The phosphoinositide coincidence detector Phafin2 promotes macropinocytosis by coordinating actin organisation at forming macropinosomes.
Bioinformatics analysis of the genes involved in the extension of prostate cancer to adjacent lymph nodes by supervised and unsupervised machine learning methods: The role of SPAG1 and PLEKHF2.
Title: Bioinformatics analysis of the genes involved in the extension of prostate cancer to adjacent lymph nodes by supervised and unsupervised machine learning methods: The role of SPAG1 and PLEKHF2.
The C-terminal acidic motif of Phafin2 inhibits PH domain binding to phosphatidylinositol 3-phosphate.
Title: The C-terminal acidic motif of Phafin2 inhibits PH domain binding to phosphatidylinositol 3-phosphate.
PtdIns(3)P binding to Phafin2 occurs with high affinity, triggering minor conformational changes in the protein. Taken together, these studies represent a platform for establishing the structural basis of Phafin2 molecular interactions and the role of the two potentially redundant PtdIns(3)P-binding domains of the protein in endomembrane compartments.
Title: Structural, thermodynamic, and phosphatidylinositol 3-phosphate binding properties of Phafin2.
These findings establish that lysosomal accumulation of Akt and Phafin2 is a critical step in the induction of autophagy via an interaction with phosphatidylinositol 3 phosphate.
Title: Lysosomal interaction of Akt with Phafin2: a critical step in the induction of autophagy.
Phafin2 controls EGFR trafficking through early endosomes by facilitating endosome fusion in concert with EEA1.
Title: The PtdIns3P-binding protein Phafin 2 mediates epidermal growth factor receptor degradation by promoting endosome fusion.
These results provide a vivid example that an endosome modulator, such as Phafin2, may control the cells' responses to the extracellular cues.
Title: Phafin2 modulates the structure and function of endosomes by a Rab5-dependent mechanism.
Results demonstrate that EAPF/Phafin-2 facilitates TNF-alpha-induced cellular apoptosis through an ER-mitochondrial apoptotic pathway.
Title: EAPF/Phafin-2, a novel endoplasmic reticulum-associated protein, facilitates TNF-alpha-triggered cellular apoptosis through endoplasmic reticulum-mitochondrial apoptotic pathway.

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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
Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102709 (e-PCR)
- UniSTS:97043

SHGC-34280 (e-PCR)
- UniSTS:6994

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in endosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome to lysosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in transport vesicle	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: pleckstrin homology domain-containing family F member 2

Names: PH and FYVE domain-containing protein 2; PH domain-containing family F member 2; endoplasmic reticulum-associated apoptosis-involved protein containing PH and FYVE domains; pleckstrin homology domain containing, family F (with FYVE domain) member 2; zinc finger FYVE domain-containing protein 18

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_024613.4 → NP_078889.1 pleckstrin homology domain-containing family F member 2

See identical proteins and their annotated locations for NP_078889.1

Status: VALIDATED

Source sequence(s)

AA767886, AC018801, AL834473

Consensus CDS

CCDS6267.1

UniProtKB/Swiss-Prot

Q9H8W4

Related

ENSP00000322373.3, ENST00000315367.4

Conserved Domains (2) summary

cd01218
Location:7 → 129

PH_Phafin2-like; Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain

cd15755
Location:148 → 211

FYVE_PKHF2; FYVE domain found in protein containing both PH and FYVE domains 2 (phafin-2) and similar proteins