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Aliases for WDFY3 Gene

Aliases for WDFY3 Gene

  • WD Repeat And FYVE Domain Containing 3 2 3 5
  • Autophagy-Linked FYVE Protein 3 4
  • ALFY 3 4
  • WD Repeat And FYVE Domain-Containing Protein 3 3
  • KIAA0993 4
  • ZFYVE25 3
  • MCPH18 3
  • BCHS 3

External Ids for WDFY3 Gene

Previous GeneCards Identifiers for WDFY3 Gene

  • GC04M085884
  • GC04M086049
  • GC04M085947
  • GC04M085809
  • GC04M085590
  • GC04M081332

Summaries for WDFY3 Gene

Entrez Gene Summary for WDFY3 Gene

  • This gene encodes a phosphatidylinositol 3-phosphate-binding protein that functions as a master conductor for aggregate clearance by autophagy. This protein shuttles from the nuclear membrane to colocalize with aggregated proteins, where it complexes with other autophagic components to achieve macroautophagy-mediated clearance of these aggregated proteins. However, it is not necessary for starvation-induced macroautophagy. [provided by RefSeq, May 2010]

GeneCards Summary for WDFY3 Gene

WDFY3 (WD Repeat And FYVE Domain Containing 3) is a Protein Coding gene. Diseases associated with WDFY3 include Microcephaly 18, Primary, Autosomal Dominant and Microcephaly. Gene Ontology (GO) annotations related to this gene include binding and beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity. An important paralog of this gene is WDFY4.

UniProtKB/Swiss-Prot for WDFY3 Gene

  • Required for selective macroautophagy (aggrephagy). Acts as an adapter protein by linking specific proteins destined for degradation to the core autophagic machinery members, such as the ATG5-ATG12-ATG16L E3-like ligase, SQSTM1 and LC3 (PubMed:20417604). Along with p62/SQSTM1, involved in the formation and autophagic degradation of cytoplasmic ubiquitin-containing inclusions (p62 bodies, ALIS/aggresome-like induced structures). Along with SQSTM1, required to recruit ubiquitinated proteins to PML bodies in the nucleus (PubMed:20168092). Important for normal brain development. Essential for the formation of axonal tracts throughout the brain and spinal cord, including the formation of the major forebrain commissures. Involved in the ability of neural cells to respond to guidance cues. Required for cortical neurons to respond to the trophic effects of netrin-1/NTN1 (By similarity). Regulates Wnt signaling through the removal of DVL3 aggregates, likely in an autophagy-dependent manner. This process may be important for the determination of brain size during embryonic development (PubMed:27008544). May regulate osteoclastogenesis by acting on the TNFSF11/RANKL - TRAF6 pathway (By similarity). After cytokinetic abscission, involved in midbody remnant degradation (PubMed:24128730). In vitro strongly binds to phosphatidylinositol 3-phosphate (PtdIns3P) (PubMed:15292400).

Gene Wiki entry for WDFY3 Gene

Additional gene information for WDFY3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDFY3 Gene

Genomics for WDFY3 Gene

GeneHancer (GH) Regulatory Elements for WDFY3 Gene

Promoters and enhancers for WDFY3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I084965 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.1 -83 2.9 PKNOX1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF213 SP3 SP5 WDFY3-AS2 WDFY3 GC04P085101
GH04I084937 Enhancer 0.7 Ensembl ENCODE 12 +27.8 27800 3.1 JUND POLR2A JUN HNF4A WDFY3-AS2 WDFY3 WDFY3-AS1 RNU6-469P
GH04I084391 Enhancer 0.3 FANTOM5 4.6 +574.6 574629 0.4 ZFP36 WDFY3 ENSG00000248749 GC04P084474
GH04I084877 Enhancer 0.7 FANTOM5 1.7 +90.2 90191 0.1 ATF1 ZBTB21 BHLHE40 CEBPB MNT ATF2 ZNF335 FOXK2 ZNF629 CREB1 WDFY3 RNU6-469P WDFY3-AS1
GH04I084951 Enhancer 0.8 ENCODE 0.4 +14.0 14017 2.4 FOXA2 SAP130 MAX SIN3A CEBPG ZNF644 YY1 GATA3 FOSL2 FOS WDFY3-AS2 WDFY3 RNU6-469P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around WDFY3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the WDFY3 gene promoter:

Genomic Locations for WDFY3 Gene

Genomic Locations for WDFY3 Gene
chr4:84,669,537-84,966,391
(GRCh38/hg38)
Size:
296,855 bases
Orientation:
Minus strand
chr4:85,590,690-85,887,544
(GRCh37/hg19)

Genomic View for WDFY3 Gene

Genes around WDFY3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDFY3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDFY3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDFY3 Gene

Proteins for WDFY3 Gene

  • Protein details for WDFY3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IZQ1-WDFY3_HUMAN
    Recommended name:
    WD repeat and FYVE domain-containing protein 3
    Protein Accession:
    Q8IZQ1
    Secondary Accessions:
    • Q4W5K5
    • Q6P0Q5
    • Q8N1T2
    • Q8NAV6
    • Q96BS7
    • Q96D33
    • Q96N85
    • Q9Y2J7

    Protein attributes for WDFY3 Gene

    Size:
    3526 amino acids
    Molecular mass:
    395258 Da
    Quaternary structure:
    • Directly interacts with ATG5 and associates with the ATG12-ATG5-ATG16L complex (PubMed:20417604). Interacts with p62/SQSTM1; this interaction is required to recruit WDFY3 to cytoplasmic bodies and to PML bodies (PubMed:20168092, PubMed:20971078). Directly interacts with GABARAP, GABARAPL1 and GABARAPL2; the interaction with GABARAP is required for WDFY3 recruitment to MAP1LC3B-positive p62/SQSTM1 bodies. Weakly interacts with MAP1LC3C; this interaction is direct. Does not interact with MAP1LC3A, nor MAP1LC3B (PubMed:24668264). Interacts with TRAF6 (By similarity).
    SequenceCaution:
    • Sequence=AAH13377.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305}; Sequence=BAB71020.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=BAC04455.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for WDFY3 Gene

    Alternative splice isoforms for WDFY3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDFY3 Gene

Post-translational modifications for WDFY3 Gene

  • Ubiquitination at isoforms=21353
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for WDFY3 Gene

Domains & Families for WDFY3 Gene

Suggested Antigen Peptide Sequences for WDFY3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IZQ1

UniProtKB/Swiss-Prot:

WDFY3_HUMAN :
  • The LIR (LC3-interacting region) motif mediates the interaction with MAP1LC3C and other ATG8 family members.
Domain:
  • The LIR (LC3-interacting region) motif mediates the interaction with MAP1LC3C and other ATG8 family members.
  • The FYVE domain mediates binding to phosphatidylinositol 3-phosphate (PtdIns3P).
genes like me logo Genes that share domains with WDFY3: view

Function for WDFY3 Gene

Molecular function for WDFY3 Gene

UniProtKB/Swiss-Prot Function:
Required for selective macroautophagy (aggrephagy). Acts as an adapter protein by linking specific proteins destined for degradation to the core autophagic machinery members, such as the ATG5-ATG12-ATG16L E3-like ligase, SQSTM1 and LC3 (PubMed:20417604). Along with p62/SQSTM1, involved in the formation and autophagic degradation of cytoplasmic ubiquitin-containing inclusions (p62 bodies, ALIS/aggresome-like induced structures). Along with SQSTM1, required to recruit ubiquitinated proteins to PML bodies in the nucleus (PubMed:20168092). Important for normal brain development. Essential for the formation of axonal tracts throughout the brain and spinal cord, including the formation of the major forebrain commissures. Involved in the ability of neural cells to respond to guidance cues. Required for cortical neurons to respond to the trophic effects of netrin-1/NTN1 (By similarity). Regulates Wnt signaling through the removal of DVL3 aggregates, likely in an autophagy-dependent manner. This process may be important for the determination of brain size during embryonic development (PubMed:27008544). May regulate osteoclastogenesis by acting on the TNFSF11/RANKL - TRAF6 pathway (By similarity). After cytokinetic abscission, involved in midbody remnant degradation (PubMed:24128730). In vitro strongly binds to phosphatidylinositol 3-phosphate (PtdIns3P) (PubMed:15292400).

Phenotypes From GWAS Catalog for WDFY3 Gene

Gene Ontology (GO) - Molecular Function for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003831 beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity IEA --
GO:0005515 protein binding IPI 18083104
GO:0005545 1-phosphatidylinositol binding IDA 15292400
GO:0008289 lipid binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with WDFY3: view
genes like me logo Genes that share phenotypes with WDFY3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for WDFY3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDFY3 Gene

Localization for WDFY3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDFY3 Gene

Nucleus membrane. Cytoplasm, cytosol. Nucleus, PML body. Membrane; Peripheral membrane protein; Cytoplasmic side. Perikaryon. Cell projection, axon. Note=Relocalization from the nucleus to the cytosol is stimulated by cellular stress, such as starvation or proteasomal inhibition. In the cytosol of starved cells, colocalizes with autophagic structures (PubMed:15292400, PubMed:20168092, PubMed:20971078, PubMed:20417604). This redistribution is dependent on p62/SQSTM1 (PubMed:20168092). When nuclear export is blocked by treatment with leptomycin B, accumulates in nuclear bodies, that completely or partially colocalize with promyelocytic leukemia (PML) bodies (PubMed:20168092). Localizes throughout neurons, including within axons. In neurons, enriched in the light membrane fraction along with the synaptosomal membrane protein synaptophysin and the membrane-bound form of LC3/MAP1LC3A/MAP1LC3B, called LC3-II, a classic marker for autophagic vesicles (By similarity). {ECO:0000250 UniProtKB:Q6VNB8, ECO:0000269 PubMed:15292400, ECO:0000269 PubMed:20168092, ECO:0000269 PubMed:20417604, ECO:0000269 PubMed:20971078}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for WDFY3 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005635 nuclear envelope IDA 15292400
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IDA,IEA 15292400
GO:0005776 autophagosome IMP,IDA 20168092
genes like me logo Genes that share ontologies with WDFY3: view

Pathways & Interactions for WDFY3 Gene

SuperPathways for WDFY3 Gene

No Data Available

Pathways by source for WDFY3 Gene

1 GeneTex pathway for WDFY3 Gene

Gene Ontology (GO) - Biological Process for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0007275 multicellular organism development IEA --
GO:0035973 aggrephagy IMP 20168092
genes like me logo Genes that share ontologies with WDFY3: view

No data available for SIGNOR curated interactions for WDFY3 Gene

Drugs & Compounds for WDFY3 Gene

No Compound Related Data Available

Transcripts for WDFY3 Gene

Unigene Clusters for WDFY3 Gene

WD repeat and FYVE domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDFY3 Gene

No ASD Table

Relevant External Links for WDFY3 Gene

GeneLoc Exon Structure for
WDFY3
ECgene alternative splicing isoforms for
WDFY3

Expression for WDFY3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WDFY3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for WDFY3 Gene

This gene is overexpressed in Pancreatic juice (25.7) and Placenta (17.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDFY3 Gene



NURSA nuclear receptor signaling pathways regulating expression of WDFY3 Gene:

WDFY3

SOURCE GeneReport for Unigene cluster for WDFY3 Gene:

Hs.480116

mRNA Expression by UniProt/SwissProt for WDFY3 Gene:

Q8IZQ1-WDFY3_HUMAN
Tissue specificity: Expressed in osteoclast and their mononuclear precursors (at protein level).

Evidence on tissue expression from TISSUES for WDFY3 Gene

  • Liver(5)
  • Blood(4.9)
  • Nervous system(4.8)
  • Kidney(4.4)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with WDFY3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDFY3 Gene

Orthologs for WDFY3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for WDFY3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WDFY3 33 34
  • 99.71 (n)
oppossum
(Monodelphis domestica)
Mammalia WDFY3 34
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia WDFY3 33 34
  • 93.2 (n)
cow
(Bos Taurus)
Mammalia WDFY3 33 34
  • 91.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia WDFY3 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Wdfy3 33 16 34
  • 86.45 (n)
rat
(Rattus norvegicus)
Mammalia Wdfy3 33
  • 85.03 (n)
chicken
(Gallus gallus)
Aves WDFY3 33 34
  • 82.09 (n)
lizard
(Anolis carolinensis)
Reptilia WDFY3 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia wdfy3 33
  • 77.2 (n)
Str.18129 33
zebrafish
(Danio rerio)
Actinopterygii wdfy3 33 34
  • 73.66 (n)
Dr.17425 33
fruit fly
(Drosophila melanogaster)
Insecta bchs 33 34
  • 53.31 (n)
worm
(Caenorhabditis elegans)
Secernentea C26H9A.2 33 34
  • 48.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BPH1 36
rice
(Oryza sativa)
Liliopsida Os.23284 33
Species where no ortholog for WDFY3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WDFY3 Gene

ENSEMBL:
Gene Tree for WDFY3 (if available)
TreeFam:
Gene Tree for WDFY3 (if available)

Paralogs for WDFY3 Gene

Paralogs for WDFY3 Gene

(6) SIMAP similar genes for WDFY3 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with WDFY3: view

Variants for WDFY3 Gene

Sequence variations from dbSNP and Humsavar for WDFY3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs193920758 uncertain-significance, Malignant tumor of prostate 84,677,403(-) G/C genic_downstream_transcript_variant, intron_variant
rs193920805 uncertain-significance, Malignant tumor of prostate 84,801,842(-) G/A/T coding_sequence_variant, missense_variant
VAR_079130 Microcephaly 18, primary, autosomal dominant (MCPH18) [MIM:617520] p.Arg2637Trp
rs878853167 uncertain-significance, not specified 84,696,004(-) CCAA/CCAACCAA coding_sequence_variant, frameshift, genic_downstream_transcript_variant
rs1000008372 -- 84,863,044(-) T/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for WDFY3 Gene

Variant ID Type Subtype PubMed ID
esv1008012 CNV insertion 20482838
esv3326890 CNV insertion 20981092
esv3601226 CNV loss 21293372
esv3601227 CNV loss 21293372
esv3601228 CNV loss 21293372
nsv1139277 CNV deletion 24896259
nsv508295 CNV deletion 20534489
nsv519588 CNV gain 19592680
nsv527581 CNV loss 19592680

Variation tolerance for WDFY3 Gene

Residual Variation Intolerance Score: 0.0964% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDFY3 Gene

Human Gene Mutation Database (HGMD)
WDFY3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDFY3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDFY3 Gene

Disorders for WDFY3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for WDFY3 Gene - From: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microcephaly 18, primary, autosomal dominant
  • mcph18
microcephaly
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards
Search WDFY3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

WDFY3_HUMAN
  • Microcephaly 18, primary, autosomal dominant (MCPH18) [MIM:617520]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH18 affected individuals manifest microcephaly with mild to moderate intellectual disability. {ECO:0000269 PubMed:27008544}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for WDFY3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with WDFY3: view

No data available for Genatlas for WDFY3 Gene

Publications for WDFY3 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. ALFY-Controlled DVL3 Autophagy Regulates Wnt Signaling, Determining Human Brain Size. (PMID: 27008544) Kadir R … Birk OS (PLoS genetics 2016) 3 4 58
  3. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. (PMID: 24668264) Lystad AH … Simonsen A (EMBO reports 2014) 3 4 58
  4. TRAF6 mediates ubiquitination of KIF23/MKLP1 and is required for midbody ring degradation by selective autophagy. (PMID: 24128730) Isakson P … Simonsen A (Autophagy 2013) 3 4 58
  5. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. (PMID: 20168092) Clausen TH … Johansen T (Autophagy 2010) 3 4 58

Products for WDFY3 Gene

Sources for WDFY3 Gene

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