WDR59
Basic information
Region (hg38): 16:74871362-75000173
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 WDR59 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 | 7 | |||||
missense | 53 | 58 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 53 | 5 | 7 |
Variants in WDR59
This is a list of pathogenic ClinVar variants found in the WDR59 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-74874248-G-A | Benign (May 21, 2018) | |||
16-74874315-G-T | not specified | Uncertain significance (Oct 24, 2024) | ||
16-74874328-T-C | not specified | Uncertain significance (Mar 07, 2024) | ||
16-74874333-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
16-74874339-C-T | not specified | Uncertain significance (Jul 31, 2024) | ||
16-74874387-A-G | not specified | Uncertain significance (Feb 27, 2024) | ||
16-74874399-G-A | not specified | Uncertain significance (May 24, 2023) | ||
16-74874417-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
16-74885659-C-G | not specified | Uncertain significance (May 05, 2023) | ||
16-74885661-T-C | not specified | Uncertain significance (Nov 13, 2024) | ||
16-74885677-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
16-74886307-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
16-74886327-C-G | not specified | Uncertain significance (Sep 27, 2024) | ||
16-74886336-C-T | not specified | Uncertain significance (Jul 05, 2024) | ||
16-74887695-C-A | Benign (Dec 31, 2019) | |||
16-74888203-C-T | not specified | Uncertain significance (May 25, 2022) | ||
16-74888204-G-A | not specified | Uncertain significance (Dec 08, 2023) | ||
16-74888208-A-G | Benign (May 21, 2018) | |||
16-74888296-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
16-74888297-G-A | not specified | Uncertain significance (Oct 07, 2022) | ||
16-74888302-C-T | not specified | Likely benign (Nov 08, 2022) | ||
16-74888308-T-C | not specified | Uncertain significance (Sep 20, 2023) | ||
16-74889799-G-A | not specified | Uncertain significance (Feb 21, 2024) | ||
16-74889808-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
16-74892508-G-A | Likely benign (Feb 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
WDR59 | protein_coding | protein_coding | ENST00000262144 | 26 | 126604 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.06e-14 | 1.00 | 125656 | 0 | 91 | 125747 | 0.000362 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.25 | 503 | 588 | 0.855 | 0.0000356 | 6374 |
Missense in Polyphen | 118 | 161.26 | 0.73176 | 1715 | ||
Synonymous | -3.66 | 291 | 222 | 1.31 | 0.0000133 | 1863 |
Loss of Function | 3.30 | 32 | 59.4 | 0.538 | 0.00000319 | 624 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000727 | 0.000726 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000324 | 0.000323 |
European (Non-Finnish) | 0.000519 | 0.000492 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000201 | 0.000196 |
Other | 0.000331 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.784
- rvis_EVS
- -1.26
- rvis_percentile_EVS
- 5.34
Haploinsufficiency Scores
- pHI
- 0.220
- hipred
- Y
- hipred_score
- 0.554
- ghis
- 0.608
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.806
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr59
- Phenotype
- limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- positive regulation of TOR signaling;cellular response to amino acid starvation
- Cellular component
- lysosomal membrane;GATOR2 complex
- Molecular function
- protein binding