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    WDFY2 WD repeat and FYVE domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 115825, updated on 28-Oct-2024

    Summary

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    Official Symbol
    WDFY2provided by HGNC
    Official Full Name
    WD repeat and FYVE domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:20482
    See related
    Ensembl:ENSG00000139668 MIM:610418; AllianceGenome:HGNC:20482
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PROF; WDF2; ZFYVE22
    Summary
    This gene encodes a protein that contains two WD domains and an FYVE zinc finger region. The function of this gene is unknown. An alternatively spliced transcript variant of this gene may exist. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 5.8), bone marrow (RPKM 4.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDFY2 in Genome Data Viewer
    Location:
    13q14.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (51584462..51767709)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (50799394..50982622)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52158598..52341845)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene microRNA 4703 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr13:52157850-52158370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5375 Neighboring gene RNA, U6 small nuclear 65, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 413, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7777 Neighboring gene RNY1 pseudogene 6 Neighboring gene ATP synthase peripheral stalk-membrane subunit b pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52200616-52201123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52201124-52201630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52201812-52202431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52202432-52203050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52216947-52217446 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52220347-52220993 Neighboring gene Sharpr-MPRA regulatory region 2859 Neighboring gene uncharacterized LOC124903177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7778 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5376 Neighboring gene dehydrogenase/reductase 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:52371189-52371717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5377 Neighboring gene uncharacterized LOC107984561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7782 Neighboring gene transmembrane protein 272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52423314-52423814 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:52435707-52436906 Neighboring gene coiled-coil domain containing 70

    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 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. WDFY2 restrains matrix metalloproteinase secretion and cell invasion by controlling VAMP3-dependent recycling. Sneeggen M, et al. Nat Commun, 2019 Jun 28. PMID 31253801, Free PMC Article
    2. Overexpression of WDFY2 inhibits prostate cancer cell growth and migration via inactivation of Akt pathway. Wang J, et al. Tumour Biol, 2017 Jun. PMID 28653900
    3. Circ_0115118 regulates endometrial functions through the miR-138-1-3p/WDFY2 axis in patients with PCOS†. Yang Z, et al. Biol Reprod, 2023 May 10. PMID 36780172
    4. P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Monti P, et al. Biosci Rep, 2019 Dec 20. PMID 31789342, Free PMC Article
    5. CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. Kannan K, et al. PLoS Genet, 2014 Mar. PMID 24675677, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ_0115118 regulates endometrial functions through the miR-138-1-3p/WDFY2 axis in patients with PCOSdagger.
      Title: Circ_0115118 regulates endometrial functions through the miR-138-1-3p/WDFY2 axis in patients with PCOS†.
    2. P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development.
      Title: P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development.
    3. WDFY2 regulates exocytosis of MT1-MMP by controlling endosomal sorting of the v-SNARE VAMP3.
      Title: WDFY2 restrains matrix metalloproteinase secretion and cell invasion by controlling VAMP3-dependent recycling.
    4. Our results showed that WDFY2 inhibited cancer cell colony formation and migration via suppressing Akt pathway, making it a potential new therapeutic target in prostate cancer.
      Title: Overexpression of WDFY2 inhibits prostate cancer cell growth and migration via inactivation of Akt pathway.
    5. CDKN2D-WDFY2 fusion could be an important molecular signature for understanding and classifying sub-lineages among heterogeneous high-grade serous ovarian carcinomas.
      Title: CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma.
    6. presence of ProF increases the PKCzeta-dependent phosphorylation of VAMP2 in vitro
      Title: WD-repeat-propeller-FYVE protein, ProF, binds VAMP2 and protein kinase Czeta.
    7. WDFY2, the WD40 and FYVE domain containing protein 2, has roles in endocytosis
      Title: The WD40 and FYVE domain containing protein 2 defines a class of early endosomes necessary for endocytosis.
    8. The ProF protein partially co-localizes with EEA1 on vesicular structures and binds to the protein kinases Akt and PKCzeta/lambda (protein kinase Czeta/lambda) via its WD-repeat propeller.
      Title: A WD-FYVE protein binds to the kinases Akt and PKCzeta/lambda.
    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

    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of fat cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    WD repeat and FYVE domain-containing protein 2
    Names
    WD40 and FYVE domain containing 2
    WD40- and FYVE domain-containing protein 2
    propeller-FYVE protein
    zinc finger FYVE domain-containing protein 22

    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_052950.4 → NP_443182.1  WD repeat and FYVE domain-containing protein 2

      See identical proteins and their annotated locations for NP_443182.1

      Status: REVIEWED

      Source sequence(s)
      AL136525, BC014004, DA124107
      Consensus CDS
      CCDS9429.1
      UniProtKB/Swiss-Prot
      B1AL86, Q96CS1, Q96P53
      Related
      ENSP00000298125.4, ENST00000298125.7
      Conserved Domains (3) summary
      cd15718
      Location:279 → 348
      FYVE_WDFY1_like; FYVE domain found in WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2, and similar proteins
      sd00039
      Location:159 → 197
      7WD40; WD40 repeat [structural motif]
      cl25539
      Location:16 → 272
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      51584462..51767709
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534915.3 → XP_011533217.1  WD repeat and FYVE domain-containing protein 2 isoform X3

      See identical proteins and their annotated locations for XP_011533217.1

      UniProtKB/TrEMBL
      Q96LK4
      Conserved Domains (5) summary
      smart00320
      Location:269 → 305
      WD40; WD40 repeats
      COG2319
      Location:13 → 305
      WD40; WD40 repeat [General function prediction only]
      cd15718
      Location:190 → 259
      FYVE_WDFY1_like; FYVE domain found in WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2, and similar proteins
      sd00039
      Location:70 → 108
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:11 → 183
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. XM_011534914.2 → XP_011533216.1  WD repeat and FYVE domain-containing protein 2 isoform X1

      Conserved Domains (4) summary
      COG2319
      Location:18 → 272
      WD40; WD40 repeat [General function prediction only]
      cd15718
      Location:279 → 348
      FYVE_WDFY1_like; FYVE domain found in WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2, and similar proteins
      sd00039
      Location:202 → 239
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:16 → 272
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. XM_047430089.1 → XP_047286045.1  WD repeat and FYVE domain-containing protein 2 isoform X4

    4. XM_024449317.2 → XP_024305085.1  WD repeat and FYVE domain-containing protein 2 isoform X2

      UniProtKB/TrEMBL
      Q96LK4
      Conserved Domains (3) summary
      cd15718
      Location:213 → 282
      FYVE_WDFY1_like; FYVE domain found in WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2, and similar proteins
      sd00039
      Location:93 → 131
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:2 → 210
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    5. XM_047430088.1 → XP_047286044.1  WD repeat and FYVE domain-containing protein 2 isoform X3

    6. XM_047430091.1 → XP_047286047.1  WD repeat and FYVE domain-containing protein 2 isoform X5

    RNA

    1. XR_007063659.1 RNA Sequence

    2. XR_941483.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      50799394..50982622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374094.1 → XP_054230069.1  WD repeat and FYVE domain-containing protein 2 isoform X3

    2. XM_054374093.1 → XP_054230068.1  WD repeat and FYVE domain-containing protein 2 isoform X1

    3. XM_054374095.1 → XP_054230070.1  WD repeat and FYVE domain-containing protein 2 isoform X4

    4. XM_054374096.1 → XP_054230071.1  WD repeat and FYVE domain-containing protein 2 isoform X5

    RNA

    1. XR_008488729.1 RNA Sequence

    2. XR_008488730.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96P53.2 GenPept UniProtKB/Swiss-Prot:Q96P53

    Gene LinkOut

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

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