WDR77
WD repeat domain 77, the group of WD repeat domain containing
Basic information
Region (hg38): 1:111439890-111449256
Links
Phenotypes
GenCC
Source:
No genCC data.
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 WDR77 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 2 | 0 |
Variants in WDR77
This is a list of pathogenic ClinVar variants found in the WDR77 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-111441267-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 1-111441283-C-T | not specified | Likely benign (Jun 24, 2022) | ||
| 1-111442029-C-G | not specified | Uncertain significance (May 17, 2023) | ||
| 1-111442083-G-C | not specified | Uncertain significance (May 17, 2023) | ||
| 1-111442657-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 1-111442711-C-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 1-111442744-C-T | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-111443384-C-A | Likely benign (Dec 01, 2022) | |||
| 1-111443385-G-A | not specified | Uncertain significance (May 14, 2024) | ||
| 1-111444074-C-T | not specified | Uncertain significance (Aug 30, 2022) | ||
| 1-111447116-C-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-111447499-T-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 1-111447556-G-C | not specified | Uncertain significance (Jun 16, 2022) | ||
| 1-111448694-C-G | Uncertain significance (Dec 01, 2022) | |||
| 1-111448715-T-C | not specified | Uncertain significance (Jun 30, 2022) | ||
| 1-111449144-A-C | not specified | Uncertain significance (Oct 03, 2023) | ||
| 1-111449147-G-A | not specified | Uncertain significance (Mar 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WDR77 | protein_coding | protein_coding | ENST00000235090 | 10 | 9487 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000245 | 0.984 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 138 | 179 | 0.772 | 0.00000838 | 2194 |
| Missense in Polyphen | 43 | 62.865 | 0.684 | 760 | ||
| Synonymous | -0.690 | 79 | 71.6 | 1.10 | 0.00000366 | 692 |
| Loss of Function | 2.13 | 9 | 19.1 | 0.472 | 8.98e-7 | 213 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000600 | 0.0000600 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000168 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000535 | 0.0000527 |
| Middle Eastern | 0.000168 | 0.000163 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Non-catalytic component of the methylosome complex, composed of PRMT5, WDR77 and CLNS1A, which modifies specific arginines to dimethylarginines in several spliceosomal Sm proteins and histones (PubMed:11756452). This modification targets Sm proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein core particles. Might play a role in transcription regulation. The methylosome complex also methylates the Piwi proteins (PIWIL1, PIWIL2 and PIWIL4), methylation of Piwi proteins being required for the interaction with Tudor domain-containing proteins and subsequent localization to the meiotic nuage (PubMed:23071334). {ECO:0000269|PubMed:11756452, ECO:0000269|PubMed:23071334}.;
- Pathway
- snRNP Assembly;RMTs methylate histone arginines;Chromatin modifying enzymes;Metabolism of RNA;Metabolism of non-coding RNA;Chromatin organization;Signaling events mediated by HDAC Class I
(Consensus)
Recessive Scores
- pRec
- 0.417
Intolerance Scores
- loftool
- 0.442
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- Y
- hipred_score
- 0.661
- ghis
- 0.604
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.937
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr77
- Phenotype
- normal 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); reproductive system phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;peptidyl-arginine N-methylation;secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development;negative regulation of epithelial cell proliferation involved in prostate gland development;positive regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;nucleoplasm;cytoplasm;Golgi apparatus;cytosol;methylosome
- Molecular function
- protein binding;methyl-CpG binding;protein-arginine N-methyltransferase activity;nuclear receptor transcription coactivator activity