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

    Gene ID: 79156, updated on 10-Dec-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 endosome and lysosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in fat (RPKM 4.0), spleen (RPKM 2.2) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLEKHF1 in Genome Data Viewer
    Location:
    19q12
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (29665461..29675477)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (32191180..32201225)
    RS_2024_09 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. Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability. Gall-Duncan T, et al. Cell, 2023 Oct 26. PMID 37827155, Free PMC Article

    See all (13) 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)

    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_2024_08

    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

    Gene LinkOut

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

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