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Aliases for WDR46 Gene

Aliases for WDR46 Gene

  • WD Repeat Domain 46 2 3 5
  • WD Repeat-Containing Protein BING4 3 4
  • C6orf11 3 4
  • BING4 3 4
  • Chromosome 6 Open Reading Frame 11 2
  • WD Repeat-Containing Protein 46 3
  • FP221 3
  • UTP7 3

External Ids for WDR46 Gene

Previous HGNC Symbols for WDR46 Gene

  • C6orf11

Previous GeneCards Identifiers for WDR46 Gene

  • GC06M033355
  • GC06Mc33315
  • GC06M033246
  • GC06M032988

Summaries for WDR46 Gene

GeneCards Summary for WDR46 Gene

WDR46 (WD Repeat Domain 46) is a Protein Coding gene. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. GO annotations related to this gene include poly(A) RNA binding.

UniProtKB/Swiss-Prot for WDR46 Gene

  • Scaffold component of the nucleolar structure. Required for localization of DDX21 and NCL to the granular compartment of the nucleolus.

Gene Wiki entry for WDR46 Gene

Additional gene information for WDR46 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDR46 Gene

Genomics for WDR46 Gene

Regulatory Elements for WDR46 Gene

Enhancers for WDR46 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H032965 1.5 ENCODE dbSUPER 91.3 +318.9 318859 10 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC ZC3H11A PPARGC1A BRD2 LEMD2 VPS52 RXRB ATF6B HCG25 RING1 DAXX WDR46 PPT2
GH06H033270 1.5 ENCODE dbSUPER 74.1 +14.4 14399 8 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D BRD2 LEMD2 VPS52 DAXX RXRB WDR46 RPS18 RING1 PHF1 RGL2
GH06H034233 1.7 Ensembl ENCODE dbSUPER 45 -952.7 -952730 17 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D LEMD2 VPS52 TAF11 WDR46 HCG25 DAXX RPS10 RGL2 ITPR3 ZBTB22
GH06H033743 1.9 FANTOM5 Ensembl ENCODE dbSUPER 38.9 -456.3 -456272 5 HDGF ARNT ZFP64 ARID4B SIN3A YBX1 FEZF1 ZNF2 YY1 SLC30A9 LEMD2 BRD2 DAXX WDR46 RPS18 VPS52 RPS10 RXRB IP6K3 UQCC2
GH06H034223 2 FANTOM5 Ensembl ENCODE dbSUPER 35.9 -934.9 -934911 2 HDGF ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 ZNF766 ZNF207 FOS VPS52 TAF11 RPS10 WDR46 LEMD2 DAXX RGL2 HCG25 ITPR3 RPL35P2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around WDR46 on UCSC Golden Path with GeneCards custom track

Promoters for WDR46 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195775 127 1601 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF766 ZNF207

Genomic Location for WDR46 Gene

33,279,103 bp from pter
33,289,527 bp from pter
10,425 bases
Minus strand

Genomic View for WDR46 Gene

Genes around WDR46 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDR46 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDR46 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for WDR46 Gene

  • Protein details for WDR46 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    WD repeat-containing protein 46
    Protein Accession:
    Secondary Accessions:
    • A6NDP5
    • Q5HYZ0
    • Q5STK5
    • Q5STR3

    Protein attributes for WDR46 Gene

    610 amino acids
    Molecular mass:
    68071 Da
    Quaternary structure:
    • Interacts with DDX21, NCL, NOP2 and EBNA1BP2.

neXtProt entry for WDR46 Gene

Post-translational modifications for WDR46 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for WDR46 Gene

No data available for DME Specific Peptides for WDR46 Gene

Domains & Families for WDR46 Gene

Gene Families for WDR46 Gene

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

Protein Domains for WDR46 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with WDR46: view

No data available for UniProtKB/Swiss-Prot for WDR46 Gene

Function for WDR46 Gene

Molecular function for WDR46 Gene

UniProtKB/Swiss-Prot Function:
Scaffold component of the nucleolar structure. Required for localization of DDX21 and NCL to the granular compartment of the nucleolus.

Phenotypes From GWAS Catalog for WDR46 Gene

Gene Ontology (GO) - Molecular Function for WDR46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
genes like me logo Genes that share ontologies with WDR46: view
genes like me logo Genes that share phenotypes with WDR46: view

Animal Model Products

CRISPR Products

miRNA for WDR46 Gene

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDR46 Gene

Localization for WDR46 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDR46 Gene

Nucleus, nucleolus.

Subcellular locations from

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 WDR46 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for WDR46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IBA --
GO:0030686 90S preribosome IBA --
genes like me logo Genes that share ontologies with WDR46: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for WDR46 Gene

Pathways & Interactions for WDR46 Gene

genes like me logo Genes that share pathways with WDR46: view

Gene Ontology (GO) - Biological Process for WDR46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA --
GO:0006364 rRNA processing TAS --
GO:1903955 positive regulation of protein targeting to mitochondrion IMP 24270810
genes like me logo Genes that share ontologies with WDR46: view

No data available for SIGNOR curated interactions for WDR46 Gene

Drugs & Compounds for WDR46 Gene

No Compound Related Data Available

Transcripts for WDR46 Gene

Unigene Clusters for WDR46 Gene

WD repeat domain 46:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDR46 Gene

No ASD Table

Relevant External Links for WDR46 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for WDR46 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for WDR46 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for WDR46 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (29.7), Blymphocyte (9.1), CD8 Tcells (7.8), Pancreas (7.4), and Testis (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDR46 Gene

Protein tissue co-expression partners for WDR46 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of WDR46 Gene:


SOURCE GeneReport for Unigene cluster for WDR46 Gene:


Evidence on tissue expression from TISSUES for WDR46 Gene

  • Nervous system(4.7)
  • Lung(4.5)
  • Liver(4.3)
  • Skin(3.5)
  • Intestine(2.5)
genes like me logo Genes that share expression patterns with WDR46: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDR46 Gene

Orthologs for WDR46 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for WDR46 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia WDR46 33 34
  • 99.73 (n)
(Bos Taurus)
Mammalia C6ORF11 34
  • 89 (a)
WDR46 33
  • 87.03 (n)
(Canis familiaris)
Mammalia WDR46 33 34
  • 86.45 (n)
(Rattus norvegicus)
Mammalia Wdr46 33
  • 84.68 (n)
(Mus musculus)
Mammalia Wdr46 33 16 34
  • 83.5 (n)
(Monodelphis domestica)
Mammalia WDR46 34
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia wdr46 33
  • 56.78 (n)
Str.7166 33
(Danio rerio)
Actinopterygii wdr46 33 34 34
  • 58.29 (n)
zgc63793 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004190 33
  • 53.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2260 33 34
  • 52.35 (n)
(Caenorhabditis elegans)
Secernentea wdr-46 33 34
  • 52.78 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C09262g 33
  • 50.98 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL034W 33
  • 50.52 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UTP7 33 34 36
  • 47.1 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G10530 33
  • 48.54 (n)
(Oryza sativa)
Liliopsida Os01g0183100 33
  • 49.44 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01502 33
  • 51.23 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC959.03c 33
  • 48.63 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
Species where no ortholog for WDR46 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 WDR46 Gene

Gene Tree for WDR46 (if available)
Gene Tree for WDR46 (if available)

Paralogs for WDR46 Gene

No data available for Paralogs for WDR46 Gene

Variants for WDR46 Gene

Sequence variations from dbSNP and Humsavar for WDR46 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000544375 -- 33,281,908(+) GGCTC(A/G)CTGCA intron-variant
rs1001113141 -- 33,283,343(+) CCCAG(C/T)ACTTT intron-variant
rs1001217115 -- 33,281,156(+) CACAA(C/G)TCATA intron-variant
rs1001311651 -- 33,281,068(+) CAAGT(C/T)TGGCT intron-variant
rs1001362190 -- 33,287,440(+) TGCCC(C/T)GATTG nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for WDR46 Gene

Variant ID Type Subtype PubMed ID
dgv10609n54 CNV loss 21841781
esv2731890 CNV deletion 23290073
esv29761 CNV loss 19812545
esv3567594 CNV deletion 23714750
esv3608627 CNV loss 21293372
esv3608628 CNV loss 21293372
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv5249 CNV deletion 18451855
nsv830634 CNV loss 17160897
nsv830635 CNV loss 17160897
nsv970109 CNV duplication 23825009

Variation tolerance for WDR46 Gene

Residual Variation Intolerance Score: 20% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.34; 81.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for WDR46 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDR46 Gene

Disorders for WDR46 Gene

Relevant External Links for WDR46

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for WDR46 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for WDR46 Gene

Publications for WDR46 Gene

  1. TAPASIN, DAXX, RGL2, HKE2 and four new genes (BING 1, 3 to 5) form a dense cluster at the centromeric end of the MHC. (PMID: 9545376) Herberg JA … Trowsdale J (Journal of molecular biology 1998) 2 3 4 60
  2. Dynamics of WD-repeat containing proteins in SSU processome components. (PMID: 24754225) Wada K … Horigome T (Biochemistry and cell biology = Biochimie et biologie cellulaire 2014) 2 3 60
  3. Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21. (PMID: 23848194) Hirai Y … Takeyasu K (Genes to cells : devoted to molecular & cellular mechanisms 2013) 3 4 60
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for WDR46 Gene

Sources for WDR46 Gene

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