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Aliases for WDR48 Gene

Aliases for WDR48 Gene

  • WD Repeat Domain 48 2 3 5
  • WD Repeat Endosomal Protein 3 4
  • UAF1 3 4
  • P80 3 4
  • Testicular Tissue Protein Li 224 3
  • WD Repeat-Containing Protein 48 3
  • USP1 Associated Factor 1 3
  • USP1-Associated Factor 1 4
  • KIAA1449 4
  • SPG60 3

External Ids for WDR48 Gene

Previous GeneCards Identifiers for WDR48 Gene

  • GC03P039069

Summaries for WDR48 Gene

Entrez Gene Summary for WDR48 Gene

  • The protein encoded by this gene has been shown to interact with ubiquitin specific peptidase 1 (USP1), activating the deubiquitinating activity of USP1 and allowing it to remove the ubiquitin moiety from monoubiquitinated FANCD2. FANCD2 is ubiquitinated in response to DNA damage. [provided by RefSeq, Sep 2016]

GeneCards Summary for WDR48 Gene

WDR48 (WD Repeat Domain 48) is a Protein Coding gene. Diseases associated with WDR48 include Autosomal Recessive Spastic Paraplegia Type 60 and Fanconi Anemia, Complementation Group A. Among its related pathways are Metabolism of proteins and Fanconi anemia pathway. An important paralog of this gene is BRWD3.

UniProtKB/Swiss-Prot for WDR48 Gene

  • Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029). Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014, PubMed:27650958, PubMed:27373336). Docks at the distal end of the USP12 fingers domain and induces a cascade of structural changes leading to the activation of the enzyme (PubMed:27650958, PubMed:27373336). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (PubMed:19075014, PubMed:27373336). In complex with USP12, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase-interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP (PubMed:12196293). In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1 (PubMed:18032488).

Additional gene information for WDR48 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDR48 Gene

Genomics for WDR48 Gene

GeneHancer (GH) Regulatory Elements for WDR48 Gene

Promoters and enhancers for WDR48 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
GH03I039050 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.0 29 2.4 HDGF HNRNPUL1 PKNOX1 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 WDR48 OXSR1 TTC21A SNORA62 GC03M039097 PIR55888
GH03I038346 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.8 -704.8 -704844 2 HDGF PKNOX1 CLOCK FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 XYLB OXSR1 GORASP1 WDR48 SCN11A PIR42930
GH03I039808 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 10.5 +757.3 757339 1.2 RB1 ARNT KLF17 SIN3A ZNF335 GLIS2 CREM NFYC ZNF398 REST MYRIP TTC21A WDR48 GORASP1 GC03M039810
GH03I039145 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 1.9 +99.1 99111 10.7 CLOCK FEZF1 DMAP1 IRF4 YY1 E2F8 ZNF143 ZNF263 SP3 MEF2D CSRNP1 ENSG00000283849 LOC101928263 GORASP1 TTC21A SNORA62 CX3CR1 XIRP1 MOBP ACVR2B-AS1
GH03I039266 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 2.5 +216.3 216305 3.4 KLF1 TEAD4 EBF1 ZNF507 FOSL1 ZNF766 POLR2A PRDM10 IKZF2 RUNX3 GORASP1 CSRNP1 XIRP1 CCR8 HNRNPA1P21 TTC21A RPSA WDR48 SLC25A38 CX3CR1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around WDR48 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the WDR48 gene promoter:

Genomic Locations for WDR48 Gene

Genomic Locations for WDR48 Gene
chr3:39,051,986-39,096,671
(GRCh38/hg38)
Size:
44,686 bases
Orientation:
Plus strand
chr3:39,093,489-39,138,155
(GRCh37/hg19)

Genomic View for WDR48 Gene

Genes around WDR48 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDR48 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDR48 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDR48 Gene

Proteins for WDR48 Gene

  • Protein details for WDR48 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TAF3-WDR48_HUMAN
    Recommended name:
    WD repeat-containing protein 48
    Protein Accession:
    Q8TAF3
    Secondary Accessions:
    • B4DM86
    • B4DQI2
    • B4DY84
    • Q63HJ2
    • Q658Y1
    • Q8N3Z1
    • Q9NSK8
    • Q9P279

    Protein attributes for WDR48 Gene

    Size:
    677 amino acids
    Molecular mass:
    76210 Da
    Quaternary structure:
    • Interacts with USP46 (PubMed:19075014, PubMed:26388029). Interacts with USP1 (PubMed:18082604, PubMed:26388029). Interacts with USP12 (PubMed:19075014, PubMed:27650958, PubMed:27373336). Component of the USP12/WDR20/WDR48 deubiquitinating complex (PubMed:27373336). Interacts with PHLPP1 (PubMed:24145035). Interacts with Saimiriine herpesvirus TIP protein (PubMed:12196293, PubMed:12885920). Interacts with papillomavirus HPV11 E1 protein (PubMed:18032488).
    Miscellaneous:
    • Knockdown of WDR48 increases Akt activation.
    SequenceCaution:
    • Sequence=AAH37168.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA95973.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAH56182.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAH56300.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for WDR48 Gene

    Alternative splice isoforms for WDR48 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDR48 Gene

Post-translational modifications for WDR48 Gene

  • Ubiquitination at posLast=106106, posLast=327327, and posLast=578578
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for WDR48 Gene

Domains & Families for WDR48 Gene

Gene Families for WDR48 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for WDR48 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TAF3

UniProtKB/Swiss-Prot:

WDR48_HUMAN :
  • N-terminal WD region interacts with TIP and C-terminal region mediates lysosomal localization (Probable). The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.
  • Belongs to the WD repeat WDR48 family.
Domain:
  • N-terminal WD region interacts with TIP and C-terminal region mediates lysosomal localization (Probable). The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.
Family:
  • Belongs to the WD repeat WDR48 family.
genes like me logo Genes that share domains with WDR48: view

Function for WDR48 Gene

Molecular function for WDR48 Gene

UniProtKB/Swiss-Prot Function:
Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029). Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014, PubMed:27650958, PubMed:27373336). Docks at the distal end of the USP12 fingers domain and induces a cascade of structural changes leading to the activation of the enzyme (PubMed:27650958, PubMed:27373336). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (PubMed:19075014, PubMed:27373336). In complex with USP12, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase-interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP (PubMed:12196293). In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1 (PubMed:18032488).

Phenotypes From GWAS Catalog for WDR48 Gene

Gene Ontology (GO) - Molecular Function for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18082604
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity TAS --
genes like me logo Genes that share ontologies with WDR48: view
genes like me logo Genes that share phenotypes with WDR48: view

Animal Model Products

miRNA for WDR48 Gene

miRTarBase miRNAs that target WDR48

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDR48 Gene

Localization for WDR48 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDR48 Gene

Nucleus. Cytoplasm. Lysosome. Late endosome. Note=Mainly in cytoplasmic compartments (PubMed:12196293, PubMed:18032488). In case of infection by papillomavirus HPV11, translocates to the nucleus via its interaction with papillomavirus HPV11 (PubMed:18032488). {ECO:0000269 PubMed:12196293, ECO:0000269 PubMed:18032488}.

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 WDR48 gene
Compartment Confidence
nucleus 5
lysosome 3
endosome 3
mitochondrion 2
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 18082604
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with WDR48: view

Pathways & Interactions for WDR48 Gene

genes like me logo Genes that share pathways with WDR48: view

Pathways by source for WDR48 Gene

Gene Ontology (GO) - Biological Process for WDR48 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007283 spermatogenesis IEA --
GO:0007338 single fertilization IEA --
GO:0008584 male gonad development IEA --
genes like me logo Genes that share ontologies with WDR48: view

No data available for SIGNOR curated interactions for WDR48 Gene

Drugs & Compounds for WDR48 Gene

No Compound Related Data Available

Transcripts for WDR48 Gene

Unigene Clusters for WDR48 Gene

WD repeat domain 48:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDR48 Gene

No ASD Table

Relevant External Links for WDR48 Gene

GeneLoc Exon Structure for
WDR48
ECgene alternative splicing isoforms for
WDR48

Expression for WDR48 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WDR48 Gene

Protein differential expression in normal tissues from HIPED for WDR48 Gene

This gene is overexpressed in Breast (21.1) and Lymph node (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDR48 Gene



Protein tissue co-expression partners for WDR48 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of WDR48 Gene:

WDR48

SOURCE GeneReport for Unigene cluster for WDR48 Gene:

Hs.109778

mRNA Expression by UniProt/SwissProt for WDR48 Gene:

Q8TAF3-WDR48_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for WDR48 Gene

  • Nervous system(5)
  • Eye(4.2)
  • Liver(4.2)
  • Stomach(4.2)
genes like me logo Genes that share expression patterns with WDR48: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDR48 Gene

Orthologs for WDR48 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for WDR48 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WDR48 33 34
  • 99.8 (n)
dog
(Canis familiaris)
Mammalia WDR48 33 34
  • 95.08 (n)
oppossum
(Monodelphis domestica)
Mammalia WDR48 34
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WDR48 34
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia WDR48 33 34
  • 93.99 (n)
rat
(Rattus norvegicus)
Mammalia Wdr48 33
  • 88.91 (n)
mouse
(Mus musculus)
Mammalia Wdr48 33 16 34
  • 88.56 (n)
chicken
(Gallus gallus)
Aves WDR48 33 34
  • 86.71 (n)
lizard
(Anolis carolinensis)
Reptilia WDR48 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia wdr48 33
  • 81.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.33731 33
zebrafish
(Danio rerio)
Actinopterygii WDR48 (3 of 3) 34
  • 91 (a)
OneToMany
WDR48 (2 of 3) 34
  • 90 (a)
OneToMany
wdr48 33 34
  • 77.6 (n)
wufd19a04 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001361 33
  • 58.05 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9062 33 34
  • 57.6 (n)
worm
(Caenorhabditis elegans)
Secernentea F35G12.4 33
  • 55.04 (n)
wdr-48 34
  • 45 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CAF4 34
  • 16 (a)
OneToMany
MDV1 34
  • 13 (a)
OneToMany
DUF1 36
thale cress
(Arabidopsis thaliana)
eudicotyledons LRS1 33
  • 49.64 (n)
rice
(Oryza sativa)
Liliopsida Os12g0165000 33
  • 49.72 (n)
Species where no ortholog for WDR48 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for WDR48 Gene

ENSEMBL:
Gene Tree for WDR48 (if available)
TreeFam:
Gene Tree for WDR48 (if available)

Paralogs for WDR48 Gene

Paralogs for WDR48 Gene

genes like me logo Genes that share paralogs with WDR48: view

Variants for WDR48 Gene

Sequence variations from dbSNP and Humsavar for WDR48 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs148407227 uncertain-significance, Hereditary spastic paraplegia 39,066,559(+) T/G coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs1000131012 -- 39,056,705(+) G/A intron_variant
rs1000146311 -- 39,094,824(+) C/A 3_prime_UTR_variant, non_coding_transcript_variant
rs1000183950 -- 39,057,044(+) C/T intron_variant
rs1000222276 -- 39,075,935(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for WDR48 Gene

Variant ID Type Subtype PubMed ID
esv2759141 CNV loss 17122850
nsv1007100 CNV loss 25217958

Variation tolerance for WDR48 Gene

Residual Variation Intolerance Score: 7.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDR48 Gene

Human Gene Mutation Database (HGMD)
WDR48
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDR48

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDR48 Gene

Disorders for WDR48 Gene

MalaCards: The human disease database

(2) MalaCards diseases for WDR48 Gene - From: Orphanet and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search WDR48 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for WDR48

genes like me logo Genes that share disorders with WDR48: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WDR48 Gene

Publications for WDR48 Gene

  1. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PMID: 24482476) Novarino G … Gleeson JG (Science (New York, N.Y.) 2014) 2 3 4 58
  2. Human papillomavirus E1 helicase interacts with the WD repeat protein p80 to promote maintenance of the viral genome in keratinocytes. (PMID: 18032488) Côté-Martin A … Archambault J (Journal of virology 2008) 3 4 22 58
  3. Herpesviral protein targets a cellular WD repeat endosomal protein to downregulate T lymphocyte receptor expression. (PMID: 12196293) Park J … Jung JU (Immunity 2002) 2 3 4 58
  4. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  5. Allosteric Activation of Ubiquitin-Specific Proteases by β-Propeller Proteins UAF1 and WDR20. (PMID: 27373336) Li H … Zheng N (Molecular cell 2016) 3 4 58

Products for WDR48 Gene

Sources for WDR48 Gene

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