WDR1
WD repeat domain 1, the group of MicroRNA protein coding host genes|WD repeat domain containing
Basic information
Region (hg38): 4:10068089-10116972
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (457 variants)
- Inborn_genetic_diseases (57 variants)
- WDR1-related_disorder (26 variants)
- Lazy_leukocyte_syndrome (13 variants)
- WDR1_deficiency (1 variants)
- Intellectual_developmental_disorder_61 (1 variants)
- not_specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017491.5. 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 | 186 | 193 | ||||
| missense | 133 | 150 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 7 | 0 | 141 | 194 | 5 |
Highest pathogenic variant AF is 0.000005541003
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WDR1 | protein_coding | protein_coding | ENST00000499869 | 15 | 42611 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.00108 | 124626 | 0 | 2 | 124628 | 0.00000802 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 275 | 381 | 0.721 | 0.0000240 | 3967 |
| Missense in Polyphen | 71 | 142.62 | 0.49782 | 1569 | ||
| Synonymous | -2.45 | 215 | 174 | 1.24 | 0.0000137 | 1149 |
| Loss of Function | 4.61 | 2 | 28.6 | 0.0699 | 0.00000131 | 342 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000580 | 0.0000580 |
| 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 | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Induces disassembly of actin filaments in conjunction with ADF/cofilin family proteins (PubMed:15629458). Enhances cofilin-mediated actin severing (By similarity). Involved in cytokinesis. Involved in chemotactic cell migration by restricting lamellipodial membrane protrusions (PubMed:18494608). Involved in myocardium sarcomere organization. Required for cardiomyocyte growth and maintenance (By similarity). Involved in megakaryocyte maturation and platelet shedding. Required for the establishment of planar cell polarity (PCP) during follicular epithelium development and for cell shape changes during PCP; the function seems to implicate cooperation with CFL1 and/or DSTN/ADF. Involved in the generation/maintenance of cortical tension (By similarity). Involved in assembly and maintenance of epithelial apical cell junctions and plays a role in the organization of the perijunctional actomyosin belt (PubMed:25792565). {ECO:0000250|UniProtKB:O88342, ECO:0000250|UniProtKB:Q9W7F2, ECO:0000269|PubMed:15629458, ECO:0000269|PubMed:18494608, ECO:0000269|PubMed:25792565}.;
- Pathway
- Hypertrophy Model;TCR;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.138
Intolerance Scores
- loftool
- rvis_EVS
- -0.57
- rvis_percentile_EVS
- 18.9
Haploinsufficiency Scores
- pHI
- 0.629
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.645
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wdr1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; hearing/vestibular/ear phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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);
Zebrafish Information Network
- Gene name
- wdr1
- Affected structure
- mandibular arch skeleton
- Phenotype tag
- abnormal
- Phenotype quality
- protruding
Gene ontology
- Biological process
- neutrophil mediated immunity;platelet degranulation;sensory perception of sound;regulation of cell shape;actin filament depolymerization;actin filament fragmentation;platelet formation;regulation of actin filament depolymerization;positive regulation of actin filament depolymerization;cortical cytoskeleton organization;locomotion;establishment of planar polarity of follicular epithelium;apical junction assembly;maintenance of epithelial cell apical/basal polarity;sarcomere organization;regulation of oligodendrocyte differentiation;regulation of ventricular cardiac muscle cell membrane repolarization;neutrophil migration
- Cellular component
- podosome;extracellular region;cytosol;plasma membrane;cell-cell junction;cell junction;cortical actin cytoskeleton;actomyosin, actin portion;cell projection;myelin sheath;extracellular exosome
- Molecular function
- actin filament binding