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    WDR54 WD repeat domain 54 [ Homo sapiens (human) ]

    Gene ID: 84058, updated on 2-Nov-2024

    Summary

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    Official Symbol
    WDR54provided by HGNC
    Official Full Name
    WD repeat domain 54provided by HGNC
    Primary source
    HGNC:HGNC:25770
    See related
    Ensembl:ENSG00000005448 MIM:620826; AllianceGenome:HGNC:25770
    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
    Summary
    Enables protein homodimerization activity. Involved in negative regulation of receptor internalization; regulation of MAPK cascade; and regulation of epidermal growth factor receptor signaling pathway. Located in intracellular membrane-bounded organelle and vesicle. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 18.8), lung (RPKM 6.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDR54 in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74421730..74425755)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74430287..74434312)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74648857..74652882)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene dynactin subunit 1 Neighboring gene DCTN1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74619101-74619643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74619644-74620185 Neighboring gene chromosome 2 open reading frame 81 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16055 Neighboring gene high mobility group AT-hook 1 pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74653567-74654066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74663701-74664380 Neighboring gene rhotekin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74666515-74667252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16056 Neighboring gene INO80B-WBP1 readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11663 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74684936-74685442 Neighboring gene INO80 complex subunit B

    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 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. Clinical significance and biological function of WD repeat domain 54 as an oncogene in colorectal cancer. Yuan Y, et al. Int J Cancer, 2019 Apr 1. PMID 29987896
    2. Transglutaminase-mediated cross-linking of WDR54 regulates EGF receptor-signaling. Maeda A, et al. Biochim Biophys Acta Mol Cell Res, 2019 Feb. PMID 30458214
    3. Inflammation-dependent overexpression of c-Myc enhances CRL4(DCAF4) E3 ligase activity and promotes ubiquitination of ST7 in colitis-associated cancer. Liu H, et al. J Pathol, 2019 Aug. PMID 30945288
    4. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Rush J, et al. Nat Biotechnol, 2005 Jan. PMID 15592455
    5. K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors. Waltho A, et al. Life Sci Alliance, 2024 Aug. PMID 38803224, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12953

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of MAPK cascade IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of epidermal growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    WD repeat-containing protein 54

    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_001320823.2 → NP_001307752.1  WD repeat-containing protein 54 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AI203710, AK023015, BG024606, BI855898
      UniProtKB/Swiss-Prot
      Q9H977
      Conserved Domains (3) summary
      COG2319
      Location:146 → 347
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:87 → 128
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:144 → 295
      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_001320824.2 → NP_001307753.1  WD repeat-containing protein 54 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses two alternate splice junctions compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AI203710, AK023015, BG024606, HY088750
      Consensus CDS
      CCDS1940.1
      UniProtKB/Swiss-Prot
      B9A049, D6W5I3, Q53H85, Q86V45, Q9H977
      Related
      ENST00000480089.5
      Conserved Domains (2) summary
      COG2319
      Location:131 → 332
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:72 → 113
      7WD40; WD40 repeat [structural motif]

    3. NM_001320825.2 → NP_001307754.1  WD repeat-containing protein 54 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (c) lacks an alternate N-terminal segment and has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AC005041, AI203710, AK023015, CD249537
      Consensus CDS
      CCDS82473.1
      UniProtKB/Swiss-Prot
      Q9H977
      UniProtKB/TrEMBL
      B9A049
      Related
      ENSP00000387236.1, ENST00000409791.5
      Conserved Domains (2) summary
      sd00039
      Location:23 → 61
      7WD40; WD40 repeat [structural motif]
      cl25539
      Location:77 → 228
      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 ...

    4. NM_032118.4 → NP_115494.1  WD repeat-containing protein 54 isoform b

      See identical proteins and their annotated locations for NP_115494.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AI203710, AK023015
      Consensus CDS
      CCDS1940.1
      UniProtKB/Swiss-Prot
      B9A049, D6W5I3, Q53H85, Q86V45, Q9H977
      Related
      ENSP00000006526.6, ENST00000348227.4
      Conserved Domains (2) summary
      COG2319
      Location:131 → 332
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:72 → 113
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      74421730..74425755
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017005064.2 → XP_016860553.1  WD repeat-containing protein 54 isoform X1

      Conserved Domains (3) summary
      COG2319
      Location:79 → 280
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:23 → 61
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:77 → 228
      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. XM_047445958.1 → XP_047301914.1  WD repeat-containing protein 54 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      74430287..74434312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344113.1 → XP_054200088.1  WD repeat-containing protein 54 isoform X1

    2. XM_054344114.1 → XP_054200089.1  WD repeat-containing protein 54 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H977.1 GenPept UniProtKB/Swiss-Prot:Q9H977

    Gene LinkOut

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

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