WDR26
Basic information
Region (hg38): 1:224385146-224437033
Links
Phenotypes
GenCC
Source:
- Skraban-Deardorff syndrome (Strong), mode of inheritance: AD
- Skraban-Deardorff syndrome (Strong), mode of inheritance: AD
- Skraban-Deardorff syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Skraban-Deardorff syndrome | AD | General | Genetic knowledge may potentially be beneficial related to manifestations such as renal issues; Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dental; Musculoskeletal; Neurologic | 28686853 |
ClinVar
This is a list of variants' phenotypes submitted to
- Skraban-Deardorff syndrome (13 variants)
- not provided (11 variants)
- Inborn genetic diseases (6 variants)
- WDR26-related disorder (1 variants)
- Intellectual disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR26 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 | 10 | |||||
missense | 10 | 93 | 111 | |||
nonsense | 8 | |||||
start loss | 0 | |||||
frameshift | 21 | 23 | ||||
inframe indel | 12 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 4 | 1 | 5 | |||
non coding | 5 | |||||
Total | 32 | 14 | 101 | 19 | 8 |
Variants in WDR26
This is a list of pathogenic ClinVar variants found in the WDR26 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-224389854-C-A | Inborn genetic diseases | Uncertain significance (Oct 26, 2017) | ||
1-224393839-T-C | not specified | Uncertain significance (Jan 05, 2023) | ||
1-224393839-TGGT-AACATTATACAAA | WDR26-related disorder | Uncertain significance (Jul 26, 2023) | ||
1-224393853-A-G | WDR26-related disorder | Likely benign (Apr 01, 2019) | ||
1-224393863-C-A | Uncertain significance (Dec 18, 2023) | |||
1-224393884-T-C | Skraban-Deardorff syndrome | Pathogenic/Likely pathogenic (Jan 06, 2023) | ||
1-224393906-T-C | not specified | Uncertain significance (Oct 22, 2018) | ||
1-224393949-T-C | not specified | Likely benign (Jun 07, 2024) | ||
1-224393959-G-A | WDR26-related disorder | Uncertain significance (Aug 03, 2023) | ||
1-224393979-T-C | Benign (Dec 31, 2019) | |||
1-224393994-C-T | Inborn genetic diseases | Pathogenic (Nov 19, 2018) | ||
1-224398108-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
1-224398112-C-T | Inborn genetic diseases | Likely benign (Jan 08, 2022) | ||
1-224398124-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
1-224398141-C-A | Uncertain significance (Jun 03, 2024) | |||
1-224398145-A-C | Uncertain significance (Sep 06, 2022) | |||
1-224398195-ACT-A | Skraban-Deardorff syndrome | Pathogenic (Aug 05, 2024) | ||
1-224398208-A-C | Uncertain significance (Oct 01, 2020) | |||
1-224398228-T-C | Pathogenic (Sep 01, 2024) | |||
1-224398256-A-C | Skraban-Deardorff syndrome | Benign (Dec 05, 2021) | ||
1-224398514-C-G | Intellectual disability | Pathogenic (Sep 10, 2020) | ||
1-224398524-TACATTTAACA-T | Inborn genetic diseases | Pathogenic (Sep 22, 2017) | ||
1-224398543-C-A | Uncertain significance (Jan 01, 2023) | |||
1-224398543-C-T | Skraban-Deardorff syndrome | Uncertain significance (Sep 13, 2019) | ||
1-224398548-A-AT | Pathogenic (Oct 23, 2020) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
WDR26 | protein_coding | protein_coding | ENST00000414423 | 14 | 51891 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.00000368 | 125568 | 0 | 10 | 125578 | 0.0000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.58 | 169 | 361 | 0.469 | 0.0000193 | 4291 |
Missense in Polyphen | 17 | 90.64 | 0.18755 | 1027 | ||
Synonymous | 1.38 | 117 | 138 | 0.850 | 0.00000713 | 1313 |
Loss of Function | 5.48 | 0 | 35.0 | 0.00 | 0.00000183 | 412 |
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) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000327 | 0.000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: G-beta-like protein involved in cell signal transduction (PubMed:15378603, PubMed:19446606, PubMed:22065575, PubMed:23625927, PubMed:27098453, PubMed:26895380). Acts as a negative regulator in MAPK signaling pathway (PubMed:15378603). Functions as a scaffolding protein to promote G beta:gamma- mediated PLCB2 plasma membrane translocation and subsequent activation in leukocytes (PubMed:22065575, PubMed:23625927). Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (PubMed:29911972). Acts as a negative regulator of the canonical Wnt signaling pathway through preventing ubiquitination of beta-catenin CTNNB1 by the beta- catenin destruction complex, thus negatively regulating CTNNB1 degradation (PubMed:27098453). Serves as a scaffold to coordinate PI3K/AKT pathway-driven cell growth and migration (PubMed:26895380). Protects cells from oxidative stress-induced apoptosis via the down-regulation of AP-1 transcriptional activity as well as by inhibiting cytochrome c release from mitochondria (PubMed:19446606). Protects also cells by promoting hypoxia- mediated autophagy and mitophagy (By similarity). {ECO:0000250|UniProtKB:F1LTR1, ECO:0000269|PubMed:15378603, ECO:0000269|PubMed:19446606, ECO:0000269|PubMed:23625927, ECO:0000269|PubMed:26895380, ECO:0000269|PubMed:27098453, ECO:0000269|PubMed:29911972}.;
- Disease
- DISEASE: Skraban-Deardorff syndrome (SKDEAS) [MIM:617616]: An autosomal dominant syndrome characterized by psychomotor developmental delay, intellectual disability with delayed speech, febrile and non-febrile seizures, abnormal gait, and facial dysmorphism. Facial features include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. {ECO:0000269|PubMed:28686853}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.04
Haploinsufficiency Scores
- pHI
- 0.946
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.614
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.662
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr26
- Phenotype
Gene ontology
- Biological process
- Cellular component
- ubiquitin ligase complex;nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol
- Molecular function
- protein binding