WDR82
Basic information
Region (hg38): 3:52254434-52288020
Previous symbols: [ "TMEM113" ]
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 WDR82 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 | 0 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in WDR82
This is a list of pathogenic ClinVar variants found in the WDR82 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-52258565-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 3-52259753-A-C | not specified | Uncertain significance (Oct 25, 2022) | ||
| 3-52259832-C-A | not specified | Uncertain significance (May 17, 2023) | ||
| 3-52260423-C-G | not specified | Uncertain significance (Nov 14, 2024) | ||
| 3-52261419-C-A | not specified | Uncertain significance (Nov 03, 2022) | ||
| 3-52261479-C-T | not specified | Likely benign (Apr 23, 2024) | ||
| 3-52278280-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 3-52278303-T-C | not specified | Uncertain significance (Jan 08, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WDR82 | protein_coding | protein_coding | ENST00000296490 | 9 | 33600 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.887 | 0.113 | 123899 | 0 | 2 | 123901 | 0.00000807 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.29 | 55 | 179 | 0.307 | 0.00000884 | 2096 |
| Missense in Polyphen | 3 | 42.026 | 0.071385 | 501 | ||
| Synonymous | 0.948 | 53 | 62.5 | 0.847 | 0.00000315 | 564 |
| Loss of Function | 3.23 | 2 | 15.9 | 0.126 | 8.03e-7 | 194 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000184 | 0.0000179 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory component of the SET1 complex implicated in the tethering of this complex to transcriptional start sites of active genes. Facilitates histone H3 'Lys-4' methylation via recruitment of the SETD1A or SETD1B to the 'Ser-5' phosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A). Component of PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. {ECO:0000269|PubMed:17998332, ECO:0000269|PubMed:18838538, ECO:0000269|PubMed:20516061}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.108
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.646
- hipred
- Y
- hipred_score
- 0.840
- ghis
- 0.637
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.902
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Wdr82
- Phenotype
Zebrafish Information Network
- Gene name
- wdr82
- Affected structure
- pharyngeal arch 1
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- histone H3-K4 methylation;histone H3-K4 trimethylation
- Cellular component
- nuclear chromosome, telomeric region;chromatin;nucleolus;histone methyltransferase complex;Set1C/COMPASS complex;PTW/PP1 phosphatase complex
- Molecular function
- chromatin binding;protein binding;histone methyltransferase activity (H3-K4 specific)