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    WDR12 WD repeat domain 12 [ Homo sapiens (human) ]

    Gene ID: 55759, updated on 7-Apr-2024

    Summary

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    Official Symbol
    WDR12provided by HGNC
    Official Full Name
    WD repeat domain 12provided by HGNC
    Primary source
    HGNC:HGNC:14098
    See related
    Ensembl:ENSG00000138442 MIM:616620; AllianceGenome:HGNC:14098
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    YTM1
    Summary
    This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein is highly similar to the mouse WD repeat domain 12 protein at the amino acid level. The protein encoded by this gene is a component of a nucleolar protein complex that affects maturation of the large ribosomal subunit.[provided by RefSeq, Dec 2008]
    Expression
    Ubiquitous expression in testis (RPKM 5.2), kidney (RPKM 3.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDR12 in Genome Data Viewer
    Location:
    2q33.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (202874261..202911673, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (203355718..203393126, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (203738984..203776396, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol glycan anchor biosynthesis class Y pseudogene Neighboring gene islet cell autoantigen 1 like Neighboring gene keratin 8 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17006 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:203790595-203791095 Neighboring gene calcium responsive transcription factor Neighboring gene keratin 8 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17008 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:203853358-203853583 Neighboring gene chromosome 18 open reading frame 32 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma. Li JL, et al. J Cell Physiol, 2020 Oct. PMID 32180229
    2. WDR12, a Member of Nucleolar PeBoW-Complex, Is Up-Regulated in Failing Hearts and Causes Deterioration of Cardiac Function. Moilanen AM, et al. PLoS One, 2015. PMID 25915632, Free PMC Article
    3. Wdr12, a mouse gene encoding a novel WD-Repeat Protein with a notchless-like amino-terminal domain. Nal B, et al. Genomics, 2002 Jan. PMID 11827460
    4. The Crystal Structure of the Ubiquitin-like Domain of Ribosome Assembly Factor Ytm1 and Characterization of Its Interaction with the AAA-ATPase Midasin. Romes EM, et al. J Biol Chem, 2016 Jan 8. PMID 26601951, Free PMC Article
    5. Interdependence of Pes1, Bop1, and WDR12 controls nucleolar localization and assembly of the PeBoW complex required for maturation of the 60S ribosomal subunit. Rohrmoser M, et al. Mol Cell Biol, 2007 May. PMID 17353269, Free PMC Article

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma.
      Title: Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma.
    2. MI associated WDR12 allele was associated significantly with diastolic dysfunction and left atrial size.
      Title: WDR12, a Member of Nucleolar PeBoW-Complex, Is Up-Regulated in Failing Hearts and Causes Deterioration of Cardiac Function.
    3. The DDX27 can interact specifically with the Pes1 and Bop1 but fulfils critical function(s) for proper 3' end formation of 47S rRNA independently of the PeBoW-complex.
      Title: DEAD-box helicase DDX27 regulates 3' end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses.
    5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Additive effect of multiple genetic variants on the risk of coronary artery disease.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
    7. WDR12 triggers accumulation of p53 in a p19ARF-independent manner in proliferating cells but not in quiescent cells.
      Title: Mammalian WDR12 is a novel member of the Pes1-Bop1 complex and is required for ribosome biogenesis and cell proliferation.
    8. Results describe the role of PeBoW-specific proteins Pes1, Bop1, and WDR12 in complex assembly and stability, nucleolar transport, and pre-ribosome association.
      Title: Interdependence of Pes1, Bop1, and WDR12 controls nucleolar localization and assembly of the PeBoW complex required for maturation of the 60S ribosomal subunit.
    Submit: New GeneRIF Correction

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
    EBI GWAS Catalog
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10881, FLJ12719, FLJ12720

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribonucleoprotein complex binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosomal large subunit biogenesis IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of PeBoW complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of PeBoW complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of preribosome, large subunit precursor IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of preribosome, large subunit precursor IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ribosome biogenesis protein WDR12
    Names
    WD repeat-containing protein 12

    NCBI Reference Sequences (RefSeq)

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    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_001371664.1 → NP_001358593.1  ribosome biogenesis protein WDR12 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC010900
      UniProtKB/TrEMBL
      B4DRY7
      Conserved Domains (2) summary
      cd00200
      Location:26 → 275
      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 ...
      sd00039
      Location:55 → 117
      7WD40; WD40 repeat [structural motif]

    2. NM_018256.4 → NP_060726.3  ribosome biogenesis protein WDR12 isoform 1

      See identical proteins and their annotated locations for NP_060726.3

      Status: REVIEWED

      Source sequence(s)
      AC010900
      Consensus CDS
      CCDS2356.1
      UniProtKB/Swiss-Prot
      B3KPA9, Q96HU0, Q9GZL7, Q9NV80, Q9NYI8
      UniProtKB/TrEMBL
      Q53T99
      Related
      ENSP00000261015.4, ENST00000261015.5
      Conserved Domains (3) summary
      cd00200
      Location:100 → 409
      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 ...
      sd00039
      Location:193 → 255
      7WD40; WD40 repeat [structural motif]
      pfam08154
      Location:4 → 70
      NLE; NLE (NUC135) domain

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      202874261..202911673 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      203355718..203393126 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9GZL7.2 GenPept UniProtKB/Swiss-Prot:Q9GZL7

    Gene LinkOut

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

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