WDR43
protein-codingWD repeat domain 43, the group of WD repeat domain containing|UTPa subcomplex|Small nucleolar RNA protein coding host genes
Gene summary
Enables RNA binding activity. Involved in positive regulation of rRNA processing; positive regulation of transcription by RNA polymerase I; and ribosomal small subunit biogenesis. Located in fibrillar center. Part of small-subunit processome. [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 ~53.6 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 WDR43 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015131.3. 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 | 3 | 1 | 4 | |||
| missense | 85 | 4 | 89 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 92 | 5 | 0 | 97 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055946.1 | 18 | MANE Select | |
| Ensembl | ENSP00000384302.3 | 18 | MANE Select | |
| Ensembl | ENSP00000296126.6 | 6 | Standard | |
| Ensembl | ENSP00000390363.1 | 1 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| wdr43 | Danio rerio | Structure: ventral wall of dorsal aorta Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
- rRNA processing
- Metabolism of RNA
- rRNA modification in the nucleus and cytosol
- rRNA processing in the nucleus and cytosol
Biological Process
- rRNA processing
- positive regulation of transcription by RNA polymerase I
- positive regulation of rRNA processing
Molecular Function
- RNA binding
- protein binding
Cellular Component
- fibrillar center
- nucleoplasm
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000407426
- Coding exons
- 18
- Length
- 53580
- Individuals with no LoFs
- 124587
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 124601
- p
- 0.0000562
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.701 | 300 | 336 | 0.892 | 0.0000159 | 4378 |
| Missense (PolyPhen) | 51 | 98.635 | 0.51706 | 1285 | ||
| Synonymous | -1.83 | 153 | 127 | 1.21 | 0.00000664 | 1238 |
| Loss of Function | 5.45 | 2 | 38.5 | 0.0519 | 0.00000186 | 504 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000083 | 0.000065 | rare |
| Latino/Admixed American | 0.000060 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00020 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000090 | 0.000071 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00051 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre- ribosomal RNA transcription by RNA polymerase I. {ECO:0000269|PubMed:17699751}.;
Intolerance Scores
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 29.31
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.420
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |