Aliases for WDFY4 Gene

Aliases for WDFY4 Gene

  • WDFY Family Member 4 2 3 5
  • WD Repeat- And FYVE Domain-Containing Protein 4 3 4
  • C10orf64 3 4
  • KIAA1607 2 4
  • Truncated WD Repeat- And FYVE Domain-Containing Protein 4 3
  • Chromosome 10 Open Reading Frame 64 2
  • Em:AC060234.3 2
  • EC 3.6.3.12 51
  • EC 3.5.1.18 51
  • FLJ45748 2
  • WDFY4 5

External Ids for WDFY4 Gene

Previous HGNC Symbols for WDFY4 Gene

  • C10orf64

Previous GeneCards Identifiers for WDFY4 Gene

  • GC10P049313
  • GC10U900444
  • GC10P049563
  • GC10P049892
  • GC10P044158

Summaries for WDFY4 Gene

GeneCards Summary for WDFY4 Gene

WDFY4 (WDFY Family Member 4) is a Protein Coding gene. Diseases associated with WDFY4 include Systemic Lupus Erythematosus. Gene Ontology (GO) annotations related to this gene include binding and phospholipid binding. An important paralog of this gene is WDFY3.

UniProtKB/Swiss-Prot Summary for WDFY4 Gene

  • Plays a critical role in the regulation of cDC1-mediated cross-presentation of viral and tumor antigens in dendritic cells. Mechanistically, acts near the plasma membrane and interacts with endosomal membranes to promote endosomal-to-cytosol antigen trafficking. Plays also a role in B-cell survival through regulation of autophagy.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for WDFY4 Gene

Genomics for WDFY4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for WDFY4 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
GH10J048683 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 600.7 +0.6 568 4 SP1 POLR2A BACH1 LARP7 ZNF143 SMAD5 TCF12 IKZF2 RCOR1 TRIM22 WDFY4 ENSG00000236800 RPL13AP19 LRRC18
GH10J048748 Enhancer 0.8 Ensembl ENCODE 16.1 +64.0 63973 2.8 PHB2 IKZF2 MNT EED HES1 FOXK2 RELB RUNX3 GATAD2B BCL11A WDFY4 RPL13AP19 MN309167 LRRC18
GH10J048701 Enhancer 1 Ensembl ENCODE dbSUPER 12.4 +20.3 20274 9.4 RAD21 FOXJ2 NFE2 CTCF USF1 SMC3 MAFG IKZF1 NR2F1 SPI1 WDFY4 ARHGAP22 ENSG00000241577 LRRC18 DRGX RPL13AP19
GH10J048759 Enhancer 0.7 FANTOM5 16 +74.4 74419 0.1 IKZF2 EED YBX1 DPF2 RELB RUNX3 POLR2A BCL11A ARNT ELF1 WDFY4 ARHGAP22 TMEM273 RPL13AP19 MN309167 LRRC18
GH10J048723 Enhancer 0.6 Ensembl dbSUPER 17.1 +39.7 39674 3 CEBPG REST SPI1 CEBPB WDFY4 VSTM4 RPL13AP19 LRRC18
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around WDFY4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for WDFY4

Top Transcription factor binding sites by QIAGEN in the WDFY4 gene promoter:
  • AML1a
  • C/EBPalpha
  • FOXD3
  • FOXL1
  • Pax-4a
  • STAT3

Genomic Locations for WDFY4 Gene

Genomic Locations for WDFY4 Gene
chr10:48,684,827-48,982,956
(GRCh38/hg38)
Size:
298,130 bases
Orientation:
Plus strand
chr10:49,892,921-50,191,001
(GRCh37/hg19)
Size:
298,081 bases
Orientation:
Plus strand

Genomic View for WDFY4 Gene

Genes around WDFY4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDFY4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDFY4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDFY4 Gene

Proteins for WDFY4 Gene

  • Protein details for WDFY4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZS81-WDFY4_HUMAN
    Recommended name:
    WD repeat- and FYVE domain-containing protein 4
    Protein Accession:
    Q6ZS81
    Secondary Accessions:
    • B9ZVP2
    • Q86WZ4
    • Q8N4A3
    • Q8TEN7
    • Q96BE1
    • Q9H7H8
    • Q9HCG5

    Protein attributes for WDFY4 Gene

    Size:
    3184 amino acids
    Molecular mass:
    353610 Da
    Quaternary structure:
    • Interacts with HSP90AB1.

    Alternative splice isoforms for WDFY4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDFY4 Gene

Selected DME Specific Peptides for WDFY4 Gene

Q6ZS81:
  • GQVIGSA
  • STVEGLQ
  • LTFFPAL

Post-translational modifications for WDFY4 Gene

  • Ubiquitination at Lys1317
  • Modification sites at PhosphoSitePlus

Domains & Families for WDFY4 Gene

Gene Families for WDFY4 Gene

Suggested Antigen Peptide Sequences for WDFY4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53625, moderately similar to WD repeat and FYVE domain-containing protein 3 (B4DWY9_HUMAN)
  • WDFY4 protein (Q6PIM1_HUMAN)
  • WD repeat- and FYVE domain-containing protein 4 (WDFY4_HUMAN)
genes like me logo Genes that share domains with WDFY4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for WDFY4 Gene

Function for WDFY4 Gene

Molecular function for WDFY4 Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in the regulation of cDC1-mediated cross-presentation of viral and tumor antigens in dendritic cells. Mechanistically, acts near the plasma membrane and interacts with endosomal membranes to promote endosomal-to-cytosol antigen trafficking. Plays also a role in B-cell survival through regulation of autophagy.

Enzyme Numbers (IUBMB) for WDFY4 Gene

Phenotypes From GWAS Catalog for WDFY4 Gene

Gene Ontology (GO) - Molecular Function for WDFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with WDFY4: view
genes like me logo Genes that share phenotypes with WDFY4: view

Animal Model Products

CRISPR Products

miRNA for WDFY4 Gene

miRTarBase miRNAs that target WDFY4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for WDFY4

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDFY4 Gene

Localization for WDFY4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDFY4 Gene

Early endosome. Endoplasmic reticulum.

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 WDFY4 gene
Compartment Confidence
plasma membrane 3
endoplasmic reticulum 3
endosome 3
cytosol 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for WDFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA --
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with WDFY4: view

Pathways & Interactions for WDFY4 Gene

PathCards logo

SuperPathways for WDFY4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for WDFY4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
genes like me logo Genes that share ontologies with WDFY4: view

No data available for Pathways by source and SIGNOR curated interactions for WDFY4 Gene

Drugs & Compounds for WDFY4 Gene

No Compound Related Data Available

Transcripts for WDFY4 Gene

mRNA/cDNA for WDFY4 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for WDFY4

Alternative Splicing Database (ASD) splice patterns (SP) for WDFY4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b · 21c ^
SP1:
SP2:
SP3: -
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 22a · 22b ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36a · 36b ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^
SP1: - - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

ExUns: 46a · 46b ^ 47 ^ 48 ^ 49a · 49b ^ 50 ^ 51 ^ 52 ^ 53 ^ 54a · 54b ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60a · 60b ^ 61 ^ 62 ^ 63 ^ 64a · 64b ^ 65 ^ 66a ·
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -

Relevant External Links for WDFY4 Gene

GeneLoc Exon Structure for
WDFY4

Expression for WDFY4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for WDFY4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Spleen (Hematopoietic System)
  • Lymph (Hematopoietic System)

mRNA differential expression in normal tissues according to GTEx for WDFY4 Gene

This gene is overexpressed in Whole Blood (x7.4) and Spleen (x6.3).

Protein differential expression in normal tissues from HIPED for WDFY4 Gene

This gene is overexpressed in Blymphocyte (21.5), Pancreas (21.3), and Brain (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for WDFY4 Gene



Protein tissue co-expression partners for WDFY4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for WDFY4

SOURCE GeneReport for Unigene cluster for WDFY4 Gene:

Hs.287379

Evidence on tissue expression from TISSUES for WDFY4 Gene

  • Spleen(4.4)
  • Nervous system(4.2)
  • Blood(4.2)
  • Lymph node(2.3)
genes like me logo Genes that share expression patterns with WDFY4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDFY4 Gene

Orthologs for WDFY4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for WDFY4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia WDFY4 30
  • 98.27 (n)
Cow
(Bos Taurus)
Mammalia WDFY4 30 31
  • 85.74 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia WDFY4 30 31
  • 85.52 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Wdfy4 30 17 31
  • 82.71 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Wdfy4 30
  • 81.52 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia WDFY4 31
  • 80 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia WDFY4 31
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves WDFY4 30 31
  • 64.24 (n)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii wdfy4 30 31
  • 54.03 (n)
OneToOne
Species where no ortholog for WDFY4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for WDFY4 Gene

ENSEMBL:
Gene Tree for WDFY4 (if available)
TreeFam:
Gene Tree for WDFY4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for WDFY4: view image

Paralogs for WDFY4 Gene

Paralogs for WDFY4 Gene

(1) SIMAP similar genes for WDFY4 Gene using alignment to 5 proteins:

  • WDFY4_HUMAN
  • F8WCU4_HUMAN
  • H3BLT2_HUMAN
  • H7BYA1_HUMAN
  • Q6PIM1_HUMAN
genes like me logo Genes that share paralogs with WDFY4: view

Variants for WDFY4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for WDFY4 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
776510 Benign: not provided 48,969,242(+) C/T SYNONYMOUS_VARIANT
778460 Benign: not provided 48,776,834(+) C/T MISSENSE_VARIANT
778461 Benign: not provided 48,817,319(+) C/T SYNONYMOUS_VARIANT
779114 Benign: not provided 48,978,340(+) T/C MISSENSE_VARIANT
781197 Benign: not provided 48,774,604(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for WDFY4 Gene

Structural Variations from Database of Genomic Variants (DGV) for WDFY4 Gene

Variant ID Type Subtype PubMed ID
dgv232e212 CNV loss 25503493
dgv453n106 CNV deletion 24896259
esv1063968 CNV deletion 17803354
esv1991692 CNV deletion 18987734
esv2472494 CNV deletion 19546169
esv2665419 CNV deletion 23128226
esv2670385 CNV deletion 23128226
esv3262829 CNV deletion 24192839
esv32989 CNV loss 17666407
esv3546252 CNV deletion 23714750
esv3623158 CNV loss 21293372
esv3623159 CNV loss 21293372
esv5318 CNV loss 18987735
esv8160 CNV gain 19470904
esv9654 CNV loss 19470904
esv999945 CNV deletion 20482838
nsv1042677 CNV loss 25217958
nsv1069480 CNV deletion 25765185
nsv1146695 CNV deletion 26484159
nsv512162 CNV loss 21212237
nsv516774 CNV loss 19592680
nsv517287 CNV loss 19592680
nsv523003 CNV loss 19592680
nsv831865 CNV gain 17160897
nsv831866 CNV gain+loss 17160897
nsv947977 CNV duplication 23825009
nsv958222 CNV deletion 24416366
nsv975799 CNV duplication 23825009

Variation tolerance for WDFY4 Gene

Gene Damage Index Score: 15.01; 96.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDFY4 Gene

Human Gene Mutation Database (HGMD)
WDFY4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDFY4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDFY4 Gene

Disorders for WDFY4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for WDFY4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
systemic lupus erythematosus
  • sle
- elite association - COSMIC cancer census association via MalaCards
Search WDFY4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for WDFY4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with WDFY4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WDFY4 Gene

Publications for WDFY4 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
  2. Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. (PMID: 22041458) Clark SL … van den Oord EJ (Psychological medicine 2012) 3 41
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. (PMID: 20169177) Yang W … Asian Lupus Genetics Consortium (PLoS genetics 2010) 3 41
  5. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. (PMID: 19838193) Han JW … Zhang XJ (Nature genetics 2009) 3 41

Products for WDFY4 Gene

  • Signalway Proteins for WDFY4

Sources for WDFY4 Gene