WDR36
Basic information
Region (hg38): 5:111092321-111130502
Previous symbols: [ "GLC1G" ]
Links
Phenotypes
GenCC
Source:
- glaucoma 1, open angle, G (Limited), mode of inheritance: Unknown
- glaucoma 1, open angle, G (Disputed Evidence), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (128 variants)
- not_provided (96 variants)
- WDR36-related_disorder (11 variants)
- Glaucoma_1,_open_angle,_G (9 variants)
- Primary_open_angle_glaucoma (5 variants)
- High_myopia (1 variants)
- Usher_syndrome_type_2C (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR36 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000139281.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | 17 | ||||
| missense | 145 | 157 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 147 | 20 | 8 |
Highest pathogenic variant AF is 0.000513148
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WDR36 | protein_coding | protein_coding | ENST00000506538 | 23 | 38787 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000572 | 0.999 | 125719 | 0 | 29 | 125748 | 0.000115 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.80 | 616 | 503 | 1.23 | 0.0000245 | 6212 |
| Missense in Polyphen | 156 | 158.27 | 0.98564 | 1997 | ||
| Synonymous | -2.69 | 223 | 177 | 1.26 | 0.00000864 | 1844 |
| Loss of Function | 4.64 | 16 | 52.1 | 0.307 | 0.00000256 | 635 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000369 | 0.000365 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000327 | 0.000326 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000711 | 0.0000703 |
| Middle Eastern | 0.000327 | 0.000326 |
| South Asian | 0.000230 | 0.000229 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the nucleolar processing of SSU 18S rRNA. Involved in T-cell activation and highly coregulated with IL2. {ECO:0000269|PubMed:21051332}.;
- Disease
- DISEASE: Glaucoma 1, open angle, G (GLC1G) [MIM:609887]: A form of primary open angle glaucoma (POAG). POAG is characterized by a specific pattern of optic nerve and visual field defects. The angle of the anterior chamber of the eye is open, and usually the intraocular pressure is increased. However, glaucoma can occur at any intraocular pressure. The disease is generally asymptomatic until the late stages, by which time significant and irreversible optic nerve damage has already taken place. {ECO:0000269|PubMed:15677485, ECO:0000269|PubMed:18172102}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- 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
(Consensus)
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- loftool
- 0.439
- rvis_EVS
- 0.03
- rvis_percentile_EVS
- 55.86
Haploinsufficiency Scores
- pHI
- 0.0995
- hipred
- N
- hipred_score
- 0.426
- ghis
- 0.617
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.893
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr36
- 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; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- wdr36
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased size
Gene ontology
- Biological process
- retina homeostasis;rRNA processing;visual perception;biological_process;regulation of axon extension;response to stimulus
- Cellular component
- cellular_component;nucleoplasm;nucleolus;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
- Molecular function
- RNA binding