WDFY2

gene
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Also known as ZFYVE22

Summary

WDFY2 (WD repeat and FYVE domain containing 2, HGNC:20482) is a protein-coding gene on chromosome 13q14.3, encoding WD repeat and FYVE domain-containing protein 2 (Q96P53). Acts in an adapter protein-like fashion to mediate the interaction between the kinase PRKCZ and its substrate VAMP2 and increases the PRKCZ-dependent phosphorylation of VAMP2.

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.

Source: NCBI Gene 115825 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_052950

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20482
Approved symbolWDFY2
NameWD repeat and FYVE domain containing 2
Location13q14.3
Locus typegene with protein product
StatusApproved
AliasesZFYVE22
Ensembl geneENSG00000139668
Ensembl biotypeprotein_coding
OMIM610418
Entrez115825

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000298125, ENST00000460145, ENST00000612477, ENST00000876143, ENST00000876144, ENST00000923031, ENST00000923032, ENST00000923033, ENST00000944287, ENST00000944288

RefSeq mRNA: 1 — MANE Select: NM_052950 NM_052950

CCDS: CCDS9429

Canonical transcript exons

ENST00000298125 — 12 exons

ExonStartEnd
ENSE000009395755166059651660663
ENSE000009395765171919851719348
ENSE000009395775172767851727790
ENSE000009395785173904951739175
ENSE000009395805175535851755459
ENSE000009395815175633251756462
ENSE000009952255170359651703650
ENSE000009952275167517051675243
ENSE000009952285175819251758300
ENSE000010926255158446251584824
ENSE000014764375175974051767709
ENSE000035984405175131051751415

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 97.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.7969 / max 956.8319, expressed in 1818 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
13519914.34521803
13520011.45171734

Top tissues by expression

260 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
upper arm skinUBERON:000426397.21gold quality
gingival epitheliumUBERON:000194994.95gold quality
epithelial cell of pancreasCL:000008394.56silver quality
gingivaUBERON:000182893.31gold quality
endothelial cellCL:000011593.27gold quality
corpus callosumUBERON:000233693.17gold quality
nippleUBERON:000203093.12gold quality
skin of legUBERON:000151192.70gold quality
kidney epitheliumUBERON:000481992.33gold quality
tibiaUBERON:000097992.26gold quality
body of pancreasUBERON:000115092.26gold quality
pancreatic ductal cellCL:000207992.12silver quality
monocyteCL:000057691.88gold quality
zone of skinUBERON:000001491.77gold quality
skin of abdomenUBERON:000141691.77gold quality
upper leg skinUBERON:000426291.48gold quality
oviduct epitheliumUBERON:000480491.28gold quality
leukocyteCL:000073891.11gold quality
esophagus squamous epitheliumUBERON:000692090.14gold quality
skin of hipUBERON:000155489.99gold quality
left ventricle myocardiumUBERON:000656689.67silver quality
synovial jointUBERON:000221789.41gold quality
substantia nigra pars reticulataUBERON:000196689.37gold quality
inferior vagus X ganglionUBERON:000536389.11gold quality
lateral globus pallidusUBERON:000247689.08gold quality
adrenal tissueUBERON:001830389.01gold quality
layer of synovial tissueUBERON:000761688.95gold quality
subthalamic nucleusUBERON:000190688.93gold quality
spermCL:000001988.87gold quality
calcaneal tendonUBERON:000370188.73gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-119yes46.36
E-ANND-3yes6.95
E-CURD-135no748.05
E-MTAB-6379no301.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting WDFY2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4682100.0068.891258
HSA-MIR-8485100.0077.574731
HSA-MIR-4673100.0066.641490
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-607799.9968.042299
HSA-MIR-480399.9871.993117
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-627-3P99.9071.423316
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-132199.8465.301811
HSA-MIR-473999.8465.251832
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-62399.7668.161170
HSA-MIR-467999.7669.191229
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-4755-5P99.7170.342716

Literature-anchored findings (GeneRIF, showing 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. (PMID:16792529)
  • WDFY2, the WD40 and FYVE domain containing protein 2, has roles in endocytosis (PMID:16873553)
  • presence of ProF increases the PKCzeta-dependent phosphorylation of VAMP2 in vitro (PMID:17313651)
  • CDKN2D-WDFY2 fusion could be an important molecular signature for understanding and classifying sub-lineages among heterogeneous high-grade serous ovarian carcinomas. (PMID:24675677)
  • 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. (PMID:28653900)
  • WDFY2 regulates exocytosis of MT1-MMP by controlling endosomal sorting of the v-SNARE VAMP3. (PMID:31253801)
  • P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. (PMID:31789342)
  • Circ_0115118 regulates endometrial functions through the miR-138-1-3p/WDFY2 axis in patients with PCOSdagger. (PMID:36780172)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriowdfy2ENSDARG00000040453
mus_musculusWdfy2ENSMUSG00000014547
rattus_norvegicusWdfy2ENSRNOG00000010042
drosophila_melanogasterStamFBGN0027363
drosophila_melanogasterGgaFBGN0030141
drosophila_melanogasterWdfy2FBGN0032246
caenorhabditis_elegansstam-1WBGENE00004109
caenorhabditis_elegansWBGENE00008402

Paralogs (10): WDFY1 (ENSG00000085449), GGA1 (ENSG00000100083), TOM1 (ENSG00000100284), GGA2 (ENSG00000103365), STAM2 (ENSG00000115145), GGA3 (ENSG00000125447), STAM (ENSG00000136738), TOM1L1 (ENSG00000141198), TOM1L2 (ENSG00000175662), HGS (ENSG00000185359)

Protein

Protein identifiers

WD repeat and FYVE domain-containing protein 2Q96P53 (reviewed: Q96P53)

Alternative names: Propeller-FYVE protein, WD40- and FYVE domain-containing protein 2, Zinc finger FYVE domain-containing protein 22

All UniProt accessions (2): Q96P53, A0A087WZX3

UniProt curated annotations — full annotation on UniProt →

Function. Acts in an adapter protein-like fashion to mediate the interaction between the kinase PRKCZ and its substrate VAMP2 and increases the PRKCZ-dependent phosphorylation of VAMP2. Positively regulates adipocyte differentiation, by facilitating the phosphorylation and thus inactivation of the anti-adipogenetic transcription factor FOXO1 by the kinase AKT1. Plays a role in endosomal control of AKT2 signaling; required for insulin-stimulated AKT2 phosphorylation and glucose uptake and insulin-stimulated phosphorylation of AKT2 substrates. Participates in transferrin receptor endocytosis.

Subunit / interactions. Homodimer. Interacts (via WD repeats 1-3) with AKT1, AKT2, PRKCZ and PRKCI. Interacts with VAMP2. Forms a complex with VAMP2 and PRKCZ. Interacts with FOXO1. Forms a complex with AKT1 and FOXO1.

Subcellular location. Endosome. Early endosome. Cytoplasm.

Domain organisation. The FYVE-type zinc finger is essential for its vesicular localization.

RefSeq proteins (1): NP_443182* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000306Znf_FYVEDomain
IPR001680WD40_rptRepeat
IPR011011Znf_FYVE_PHDHomologous_superfamily
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR017455Znf_FYVE-relDomain
IPR019775WD40_repeat_CSConserved_site
IPR020472WD40_PAC1Repeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR042234WDFY1/WDFY2Family

Pfam: PF00400, PF01363

UniProt features (19 total): binding site 8, repeat 7, sequence conflict 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96P53-F194.330.94

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 290; 314; 317; 322; 325; 344; 347; 287

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 173 (showing top): GOBP_REGULATION_OF_FAT_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_POSITIVE_REGULATION_OF_FAT_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, LIAO_METASTASIS, GOBP_FAT_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, RIGGI_EWING_SARCOMA_PROGENITOR_UP, GOBP_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, chr13q14, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, GOBP_POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_REGULATION_OF_PROTEIN_MODIFICATION_PROCESS, GOBP_REGULATION_OF_PROTEIN_METABOLIC_PROCESS

GO Biological Process (2): positive regulation of protein phosphorylation (GO:0001934), positive regulation of fat cell differentiation (GO:0045600)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): early endosome (GO:0005769), vesicle (GO:0031982), cytoplasm (GO:0005737), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of protein phosphorylation1
protein phosphorylation1
positive regulation of protein modification process1
positive regulation of phosphorylation1
fat cell differentiation1
positive regulation of cell differentiation1
regulation of fat cell differentiation1
transition metal ion binding1
binding1
cation binding1
endosome1
membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

1696 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
WDFY2TFRCP02786687
WDFY2WDFY4Q6ZS81578
WDFY2AKT1P31749544
WDFY2CATSPERZQ9NTU4526
WDFY2SERPINE3A8MV23510
WDFY2TBC1D31Q96DN5488
WDFY2CLDN15P56746485
WDFY2CDC123O75794478
WDFY2APPL1Q9UKG1470
WDFY2SLC17A5Q9NRA2464
WDFY2CMC2Q9NRP2440
WDFY2CDKL1Q00532440
WDFY2NOL10Q9BSC4438
WDFY2EEA1Q15075437
WDFY2CDKN2DP55273428

IntAct

22 interactions, top by confidence:

ABTypeScore
ARL6IP1WDFY2psi-mi:“MI:0915”(physical association)0.560
WDFY2RPRMpsi-mi:“MI:0915”(physical association)0.560
YIF1AWDFY2psi-mi:“MI:0915”(physical association)0.560
SYPWDFY2psi-mi:“MI:0915”(physical association)0.560
WDFY2NUDCpsi-mi:“MI:0915”(physical association)0.560
DAP3PNMA6Apsi-mi:“MI:0914”(association)0.530
PNOCCETN3psi-mi:“MI:0914”(association)0.530
WDFY2U2SURPpsi-mi:“MI:0914”(association)0.350
ATG16L1ESYT2psi-mi:“MI:0914”(association)0.350
RBM17psi-mi:“MI:0914”(association)0.350
SLC7A3ILVBLpsi-mi:“MI:0914”(association)0.350
WDFY2ARL6IP1psi-mi:“MI:0915”(physical association)0.000
WDFY2YIF1Apsi-mi:“MI:0915”(physical association)0.000
WDFY2RPRMpsi-mi:“MI:0915”(physical association)0.000
WDFY2SYPpsi-mi:“MI:0915”(physical association)0.000

BioGRID (77): ERCC6L (Affinity Capture-MS), PALLD (Affinity Capture-MS), RBM17 (Affinity Capture-MS), RUFY1 (Affinity Capture-MS), RBM26 (Affinity Capture-MS), UTP6 (Affinity Capture-MS), GPD2 (Affinity Capture-MS), U2SURP (Affinity Capture-MS), MESDC2 (Affinity Capture-MS), NUP54 (Affinity Capture-MS), NFXL1 (Affinity Capture-MS), C2CD5 (Affinity Capture-MS), CHERP (Affinity Capture-MS), CCDC51 (Affinity Capture-MS), EFNB1 (Affinity Capture-MS)

ESM2 similar proteins: A0AUS0, A8XXC7, B3RQN1, B6K7R8, C5DF48, E9Q4P1, F4INY4, G5EEG7, O74453, O94394, P38123, P62883, P62884, Q18964, Q25306, Q2KIY3, Q2TAY7, Q2TBS9, Q38SD2, Q3EBD3, Q3MKM6, Q3UHC2, Q3UKJ7, Q5FVN8, Q5JTN6, Q5ZMC3, Q5ZME8, Q67UX0, Q6C953, Q6NRT3, Q6TNS2, Q76B40, Q7ZVA0, Q8BUB4, Q8H594, Q8IWB7, Q8N9V3, Q8SRB0, Q8W117, Q91WQ5

Diamond homologs: A0A0D1E015, A0JMD2, A1CEK1, A1DFP5, A2QWA2, A3LX75, A4QTV1, A4RF61, A8QCE4, A8XJZ8, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, E9Q4P1, O12940, O13821, O14964, O60784, O76902, O88746, P0CR78, P0CR79, P0CS26, P0CS27, P40343, P87157, Q0CJV3, Q0P4S0, Q0U4Z8, Q0V8S0, Q10410, Q13615, Q15075

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

53 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3391 predictions. Top by Δscore:

VariantEffectΔscore
13:51584824:GGT:Gdonor_loss1.0000
13:51584825:G:Tdonor_loss1.0000
13:51584826:T:Gdonor_loss1.0000
13:51675244:G:GGdonor_gain1.0000
13:51703590:TTACA:Tacceptor_loss1.0000
13:51703591:TACAG:Tacceptor_loss1.0000
13:51703593:CA:Cacceptor_loss1.0000
13:51703594:A:AGacceptor_gain1.0000
13:51703595:G:GGacceptor_gain1.0000
13:51703595:G:GTacceptor_loss1.0000
13:51703595:GGA:Gacceptor_gain1.0000
13:51739176:G:GGdonor_gain1.0000
13:51751308:A:AGacceptor_gain1.0000
13:51751309:G:GGacceptor_gain1.0000
13:51751309:GC:Gacceptor_gain1.0000
13:51751412:GGAG:Gdonor_gain1.0000
13:51751413:GAGG:Gdonor_gain1.0000
13:51751414:AGGTA:Adonor_loss1.0000
13:51751415:GGTA:Gdonor_loss1.0000
13:51751416:G:GAdonor_loss1.0000
13:51755355:A:AGacceptor_gain1.0000
13:51755356:A:Gacceptor_gain1.0000
13:51756458:GAAGA:Gdonor_gain1.0000
13:51756460:AGA:Adonor_gain1.0000
13:51756461:GA:Gdonor_gain1.0000
13:51756461:GAG:Gdonor_gain1.0000
13:51756462:AG:Adonor_loss1.0000
13:51756463:G:GGdonor_gain1.0000
13:51756464:TAA:Tdonor_loss1.0000
13:51584825:G:GGdonor_gain0.9900

AlphaMissense

2650 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:51739126:T:AW226R1.000
13:51739126:T:CW226R1.000
13:51739128:G:CW226C1.000
13:51739128:G:TW226C1.000
13:51751389:T:AW269R1.000
13:51751389:T:CW269R1.000
13:51755367:T:AW281R1.000
13:51755367:T:CW281R1.000
13:51755369:G:CW281C1.000
13:51755369:G:TW281C1.000
13:51755385:T:AC287S1.000
13:51755385:T:CC287R1.000
13:51755386:G:AC287Y1.000
13:51755386:G:CC287S1.000
13:51755387:C:GC287W1.000
13:51755406:T:CF294L1.000
13:51755408:C:AF294L1.000
13:51755408:C:GF294L1.000
13:51755412:T:AW296R1.000
13:51755412:T:CW296R1.000
13:51755414:G:CW296C1.000
13:51755414:G:TW296C1.000
13:51755455:G:CR310T1.000
13:51755456:A:CR310S1.000
13:51755456:A:TR310S1.000
13:51756332:C:GH312D1.000
13:51756335:C:GH313D1.000
13:51756337:C:AH313Q1.000
13:51756337:C:GH313Q1.000
13:51756338:T:AC314S1.000

dbSNP variants (sampled 300 via entrez): RS1000016727 (13:51625859 A>G), RS1000029056 (13:51672015 C>A), RS1000033571 (13:51653070 A>G), RS1000050857 (13:51695753 C>G,T), RS1000057081 (13:51685475 G>A,T), RS1000062895 (13:51679002 A>C), RS1000081347 (13:51608636 G>A,C), RS1000120137 (13:51586517 T>C), RS1000133711 (13:51658988 G>A,T), RS1000155429 (13:51614135 A>G), RS1000172116 (13:51752604 G>A,C), RS1000177014 (13:51754988 T>C), RS1000178189 (13:51717152 A>G), RS1000179457 (13:51703403 T>A), RS1000204621 (13:51753017 G>T)

Disease associations

OMIM: gene MIM:610418 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009440_14Age-related cognitive decline (attention/processing speed) (slope of z-scores)4.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007710cognitive decline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases methylation2
aristolochic acid Idecreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Adecreases methylation1
methylparabenincreases expression1
sodium arseniteaffects methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
aflatoxin B2decreases methylation1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
bisphenol Sdecreases methylation1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Leflunomideincreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Air Pollutantsaffects cotreatment, decreases expression, increases abundance1
Arsenicaffects methylation1
Calcitriolincreases expression, affects cotreatment1
Diazinonincreases methylation1
Hydrogen Peroxidedecreases expression1
Ozoneaffects cotreatment, decreases expression, increases abundance1
Plant Extractsaffects cotreatment, increases expression1
Testosteroneaffects cotreatment, increases expression1
Dronabinolincreases expression1
1-Methyl-4-phenylpyridiniumincreases expression1
Cyclosporineincreases expression1

Cellosaurus cell lines

7 cell lines: 7 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_3768OV-90Cancer cell lineFemale
CVCL_4Z23OV90C-ACancer cell lineFemale
CVCL_4Z24OV90C-DCancer cell lineFemale
CVCL_4Z25OV90D-6Cancer cell lineFemale
CVCL_4Z26OV90D-7Cancer cell lineFemale
CVCL_4Z27OV90P-3Cancer cell lineFemale
CVCL_4Z28OV90P-7Cancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.