WDR6
Basic information
Region (hg38): 3:49007062-49015953
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR6 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 88 | 93 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 7 | |||||
Total | 0 | 0 | 94 | 6 | 1 |
Variants in WDR6
This is a list of pathogenic ClinVar variants found in the WDR6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-49007356-G-C | Likely benign (Mar 01, 2022) | |||
3-49007427-T-G | not specified | Uncertain significance (Jul 13, 2021) | ||
3-49011646-G-A | not specified | Uncertain significance (Jan 24, 2023) | ||
3-49011739-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
3-49011745-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
3-49011746-G-A | not specified | Uncertain significance (Sep 30, 2024) | ||
3-49011766-C-A | not specified | Uncertain significance (Jun 04, 2024) | ||
3-49011860-G-A | not specified | Uncertain significance (May 30, 2023) | ||
3-49011862-T-C | not specified | Uncertain significance (Jun 07, 2023) | ||
3-49012050-G-T | not specified | Uncertain significance (Jun 02, 2023) | ||
3-49012094-G-C | not specified | Uncertain significance (Oct 01, 2024) | ||
3-49012105-A-G | not specified | Likely benign (Jan 03, 2024) | ||
3-49012126-C-T | not specified | Uncertain significance (May 30, 2024) | ||
3-49012157-A-G | not specified | Uncertain significance (Jan 26, 2023) | ||
3-49012203-G-C | not specified | Uncertain significance (Oct 17, 2023) | ||
3-49012231-G-A | not specified | Uncertain significance (May 12, 2024) | ||
3-49012231-G-T | not specified | Uncertain significance (Jan 24, 2024) | ||
3-49012235-G-A | not specified | Uncertain significance (Apr 26, 2023) | ||
3-49012312-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
3-49012324-G-A | not specified | Uncertain significance (Oct 02, 2023) | ||
3-49012429-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
3-49012447-G-A | not specified | Uncertain significance (Nov 03, 2023) | ||
3-49012484-G-C | not specified | Uncertain significance (Dec 08, 2021) | ||
3-49012500-T-G | not specified | Uncertain significance (May 11, 2022) | ||
3-49012532-G-A | not specified | Uncertain significance (Oct 16, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
WDR6 | protein_coding | protein_coding | ENST00000395474 | 6 | 8892 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.14e-9 | 0.999 | 125671 | 0 | 77 | 125748 | 0.000306 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.799 | 631 | 690 | 0.914 | 0.0000421 | 7391 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000536 | 0.000536 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.000186 | 0.000185 |
European (Non-Finnish) | 0.000317 | 0.000316 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.000460 | 0.000457 |
Other | 0.000490 | 0.000489 |
dbNSFP
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
Haploinsufficiency Scores
- pHI
- 0.0949
- hipred
- N
- hipred_score
- 0.372
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.577
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr6
- Phenotype
Gene ontology
- Biological process
- cell cycle arrest;negative regulation of cell population proliferation;negative regulation of autophagy
- Cellular component
- cytoplasm;cytosol;plasma membrane;COP9 signalosome
- Molecular function
- RNA binding;protein binding