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

Gene ID: 115825, updated on 2-Nov-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
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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

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