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

Gene ID: 84058, updated on 5-Mar-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 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 vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 18.8), lung (RPKM 6.6) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
2p13.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74421730..74425755)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74430287..74434312)
105.20220307 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
  • 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. Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. Li X, et al. Mol Cell Proteomics, 2016 Sep. PMID 27432908, Free PMC Article

See all (19) 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 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_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
    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

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