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PLEKHF1 pleckstrin homology and FYVE domain containing 1 [ Homo sapiens (human) ]

Gene ID: 79156, updated on 5-Mar-2024

Summary

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Official Symbol
PLEKHF1provided by HGNC
Official Full Name
pleckstrin homology and FYVE domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20764
See related
Ensembl:ENSG00000166289 MIM:615200; AllianceGenome:HGNC:20764
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
APPD; LAPF; PHAFIN1; ZFYVE15
Summary
Enables phosphatidylinositol-3-phosphate binding activity; phosphatidylinositol-4-phosphate binding activity; and phosphatidylinositol-5-phosphate binding activity. Involved in endosome organization; positive regulation of autophagy; and protein localization to plasma membrane. Located in lysosome. Colocalizes with endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 4.0), spleen (RPKM 2.2) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
19q12
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (29665461..29675477)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (32191180..32201225)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (30156368..30166384)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:30100801-30101312 Neighboring gene POP4 homolog, ribonuclease P/MRP subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14409 Neighboring gene Sharpr-MPRA regulatory region 12961 Neighboring gene uncharacterized LOC105372353 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:30156127-30156680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:30156681-30157234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14413 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:30181190-30181742 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:30181743-30182294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14416 Neighboring gene chromosome 19 open reading frame 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14418 Neighboring gene uncharacterized LOC107985345 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:30219444-30219638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14420

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. Lysosomal targeting of phafin1 mediated by Rab7 induces autophagosome formation. Lin WJ, et al. Biochem Biophys Res Commun, 2012 Jan 6. PMID 22115783
  2. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Haney MS, et al. Nat Genet, 2018 Dec. PMID 30397336, Free PMC Article
  3. Towards a proteome-scale map of the human protein-protein interaction network. Rual JF, et al. Nature, 2005 Oct 20. PMID 16189514
  4. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Maruyama K, et al. Gene, 1994 Jan 28. PMID 8125298
  5. Toward a confocal subcellular atlas of the human proteome. Barbe L, et al. Mol Cell Proteomics, 2008 Mar. PMID 18029348

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4090

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 phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-4-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylinositol-5-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in endosome organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endosome to lysosome transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of intrinsic apoptotic signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vesicle organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome membrane IC
Inferred by Curator
more info
 PubMed 
located_in lysosomal membrane IC
Inferred by Curator
more info
 PubMed 
is_active_in lysosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pleckstrin homology domain-containing family F member 1
Names
PH and FYVE domain-containing protein 1
PH domain-containing family F member 1
apoptosis-inducing protein D
lysosome-associated apoptosis-inducing protein containing PH and FYVE domains
phafin 1
pleckstrin homology domain containing, family F (with FYVE domain) member 1
zinc finger FYVE domain-containing protein 15

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_024310.5 → NP_077286.3  pleckstrin homology domain-containing family F member 1

    See identical proteins and their annotated locations for NP_077286.3

    Status: VALIDATED

    Source sequence(s)
    AY037145, BC018876
    Consensus CDS
    CCDS12417.1
    UniProtKB/Swiss-Prot
    Q96K11, Q96S99, Q9BUB9
    Related
    ENSP00000389787.2, ENST00000436066.4
    Conserved Domains (2) summary
    cd01218
    Location:7 → 129
    PH_Phafin2-like; Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain
    cd15754
    Location:148 → 211
    FYVE_PKHF1; FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1) 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
    29665461..29675477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259256.4 → XP_005259313.1  pleckstrin homology domain-containing family F member 1 isoform X1

    See identical proteins and their annotated locations for XP_005259313.1

    UniProtKB/TrEMBL
    B4DWN9
    Conserved Domains (3) summary
    cd01218
    Location:92 → 214
    PH_Phafin2-like; Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain
    cd15754
    Location:233 → 296
    FYVE_PKHF1; FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1) and similar proteins
    pfam00169
    Location:124 → 216
    PH; PH domain

  2. XM_011527309.4 → XP_011525611.1  pleckstrin homology domain-containing family F member 1 isoform X2

    See identical proteins and their annotated locations for XP_011525611.1

    UniProtKB/Swiss-Prot
    Q96K11, Q96S99, Q9BUB9
    Conserved Domains (2) summary
    cd01218
    Location:7 → 129
    PH_Phafin2-like; Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain
    cd15754
    Location:148 → 211
    FYVE_PKHF1; FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    32191180..32201225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322135.1 → XP_054178110.1  pleckstrin homology domain-containing family F member 1 isoform X1

    UniProtKB/TrEMBL
    B4DWN9

  2. XM_054322134.1 → XP_054178109.1  pleckstrin homology domain-containing family F member 1 isoform X2

    UniProtKB/Swiss-Prot
    Q96K11, Q96S99, Q9BUB9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96S99.3 GenPept UniProtKB/Swiss-Prot:Q96S99

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