WDR55
protein-codingWD repeat domain 55, the group of WD repeat domain containing
Gene summary
Predicted to be involved in rRNA processing. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to WDR55 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017706.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 68 | 3 | 71 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 68 | 4 | 0 | 72 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060176.3 | 7 | MANE Select | |
| Ensembl | ENSP00000351100.5 | 7 | MANE Select | |
| Ensembl | ENSP00000439719.1 | 4 | Standard | |
| Ensembl | ENSP00000426304.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| wdr55 | Danio rerio | Structure: anatomical system Quality: quality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- rRNA processing
- biological_process
Molecular Function
- molecular_function
Cellular Component
- cellular_component
- nucleolus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000358337
- Coding exons
- 7
- Length
- 9449
- Individuals with no LoFs
- 125634
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 114
- Defined
- 125748
- p
- 0.000453
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.972 | 186 | 227 | 0.819 | 0.0000125 | 2500 |
| Missense (PolyPhen) | 54 | 74.454 | 0.72528 | 816 | ||
| Synonymous | 0.973 | 73 | 84.4 | 0.865 | 0.00000419 | 783 |
| Loss of Function | -0.550 | 19 | 16.6 | 1.15 | 9.60e-7 | 172 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00073 | 0.00072 | rare |
| Ashkenazi Jewish | 0.00070 | 0.00069 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00055 | 0.00055 | rare |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Nucleolar protein that acts as a modulator of rRNA synthesis. Plays a central role during organogenesis (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.59
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.234
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |