U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

WDR46 WD repeat domain 46 [ Homo sapiens (human) ]

Gene ID: 9277, updated on 3-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
WDR46provided by HGNC
Official Full Name
WD repeat domain 46provided by HGNC
Primary source
HGNC:HGNC:13923
See related
Ensembl:ENSG00000227057 MIM:611440; AllianceGenome:HGNC:13923
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UTP7; BING4; FP221; C6orf11
Summary
Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in appendix (RPKM 10.6), testis (RPKM 10.3) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See WDR46 in Genome Data Viewer
Location:
6p21.32
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33279108..33289239, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33100470..33110601, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33246885..33257016, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33244298-33245030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33245765-33246496 Neighboring gene beta-1,3-galactosyltransferase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33255009-33255542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33255543-33256076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33256611-33257144 Neighboring gene microRNA 6873 Neighboring gene microRNA 6834 Neighboring gene prefoldin subunit 6 Neighboring gene ral guanine nucleotide dissociation stimulator like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33265070-33265597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33265684-33266184 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33266952-33267130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33267887-33268394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33268395-33268900 Neighboring gene TAP binding protein

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21. Hirai Y, et al. Genes Cells, 2013 Sep. PMID 23848194
  2. WDR46 is a Genetic Risk Factor for Aspirin-Exacerbated Respiratory Disease in a Korean Population. Pasaje CF, et al. Allergy Asthma Immunol Res, 2012 Jul. PMID 22754713, Free PMC Article
  3. Dynamics of WD-repeat containing proteins in SSU processome components. Wada K, et al. Biochem Cell Biol, 2014 Jun. PMID 24754225
  4. Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHC. Herberg JA, et al. Eur J Immunol, 1998 Feb. PMID 9521053
  5. TAPASIN, DAXX, RGL2, HKE2 and four new genes (BING 1, 3 to 5) form a dense cluster at the centromeric end of the MHC. Herberg JA, et al. J Mol Biol, 1998 Apr 10. PMID 9545376

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. When WDR46 was knocked down, nucleolin and DDX21 were mislocalized from the granular component to the edges of the nucleoli.
    Title: Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
Process Evidence Code Pubs
involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosomal small subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of small-subunit processome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
WD repeat-containing protein 46
Names
WD repeat-containing protein BING4

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001164267.2 → NP_001157739.1  WD repeat-containing protein 46 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK292171, AK298151, BC000388, BX439421
    UniProtKB/TrEMBL
    A0A1U9X8U7, A0A1U9X8W1
    Conserved Domains (3) summary
    smart01033
    Location:386 → 464
    BING4CT; BING4CT (NUC141) domain
    sd00039
    Location:145 → 181
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:154 → 333
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. NM_005452.6 → NP_005443.3  WD repeat-containing protein 46 isoform 1

    See identical proteins and their annotated locations for NP_005443.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK292171, BC000388, DB272479
    Consensus CDS
    CCDS4772.1
    UniProtKB/Swiss-Prot
    A6NDP5, O15213, Q5HYZ0, Q5STK5, Q5STR3
    UniProtKB/TrEMBL
    B0UZZ8, E7EM79
    Related
    ENSP00000363746.4, ENST00000374617.9
    Conserved Domains (4) summary
    smart01033
    Location:440 → 518
    BING4CT; BING4CT (NUC141) domain
    COG2319
    Location:203 → 396
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:199 → 235
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:208 → 387
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    33279108..33289239 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419523.1 → XP_047275479.1  WD repeat-containing protein 46 isoform X1

  2. XM_047419524.1 → XP_047275480.1  WD repeat-containing protein 46 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    4690589..4700724 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329929.1 → XP_054185904.1  WD repeat-containing protein 46 isoform X1

  2. XM_054329930.1 → XP_054185905.1  WD repeat-containing protein 46 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    4522622..4532757 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330422.1 → XP_054186397.1  WD repeat-containing protein 46 isoform X1

  2. XM_054330423.1 → XP_054186398.1  WD repeat-containing protein 46 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    4715074..4725175 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330915.1 → XP_054186890.1  WD repeat-containing protein 46 isoform X1

  2. XM_054330916.1 → XP_054186891.1  WD repeat-containing protein 46 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    4473279..4483663 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331195.1 → XP_054187170.1  WD repeat-containing protein 46 isoform X4

  2. XM_054331194.1 → XP_054187169.1  WD repeat-containing protein 46 isoform X3

  3. XM_054331196.1 → XP_054187171.1  WD repeat-containing protein 46 isoform X1

  4. XM_054331197.1 → XP_054187172.1  WD repeat-containing protein 46 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33100470..33110601 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356755.1 → XP_054212730.1  WD repeat-containing protein 46 isoform X1

  2. XM_054356756.1 → XP_054212731.1  WD repeat-containing protein 46 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15213.3 GenPept UniProtKB/Swiss-Prot:O15213

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous