WDR6
protein-codingWD repeat domain 6, the group of WD repeat domain containing
Gene 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. The encoded protein interacts with serine/threonine kinase 11, and is implicated in cell growth arrest. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.9 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 WDR6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018031.6. 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 | 170 | 6 | 176 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 173 | 6 | 0 | 179 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060501.4 | 6 | MANE Select | |
| Ensembl | ENSP00000477389.1 | 6 | MANE Select | |
| RefSeq | NP_001307475.1 | 5 | Standard | |
| RefSeq | NP_001307476.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell cycle arrest
- negative regulation of cell population proliferation
- negative regulation of autophagy
Molecular Function
- RNA binding
- protein binding
Cellular Component
- cytoplasm
- cytosol
- plasma membrane
- COP9 signalosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395474
- Coding exons
- 6
- Length
- 8892
- Individuals with no LoFs
- 125671
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 77
- Defined
- 125748
- p
- 0.000306
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.799 | 631 | 690 | 0.914 | 0.0000421 | 7391 |
| Missense (PolyPhen) | 179 | 207.49 | 0.86267 | 2221 | ||
| Synonymous | -0.144 | 277 | 274 | 1.01 | 0.0000151 | 2538 |
| Loss of Function | 2.87 | 21 | 40.8 | 0.515 | 0.00000268 | 387 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00046 | 0.00046 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Enhances the STK11/LKB1-induced cell growth suppression activity. Negative regulator of amino acid starvation-induced autophagy. {ECO:0000269|PubMed:17216128, ECO:0000269|PubMed:22354037}.;
Recessive Scores
- pRec
- 0.0981
Intolerance Scores
- LoFtool
- 0.803
- RVIS EVS
- -1.43
- RVIS percentile EVS
- 4.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.577
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |