VIL1
villin 1, the group of Gelsolin/villins
Basic information
Region (hg38): 2:218419121-218453295
Previous symbols: [ "VIL" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (107 variants)
- VIL1-related_disorder (14 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VIL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007127.3. 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 | 5 | |||||
| missense | 105 | 115 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 106 | 9 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VIL1 | protein_coding | protein_coding | ENST00000248444 | 19 | 34204 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.64e-14 | 0.959 | 125638 | 0 | 109 | 125747 | 0.000434 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.901 | 436 | 492 | 0.886 | 0.0000285 | 5439 |
| Missense in Polyphen | 128 | 153.08 | 0.83618 | 1767 | ||
| Synonymous | 0.346 | 197 | 203 | 0.969 | 0.0000129 | 1597 |
| Loss of Function | 2.32 | 29 | 45.9 | 0.631 | 0.00000231 | 489 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00177 | 0.00173 |
| Ashkenazi Jewish | 0.000102 | 0.0000992 |
| East Asian | 0.000272 | 0.000217 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000353 | 0.000352 |
| Middle Eastern | 0.000272 | 0.000217 |
| South Asian | 0.000734 | 0.000719 |
| Other | 0.000817 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Epithelial cell-specific Ca(2+)-regulated actin- modifying protein that modulates the reorganization of microvillar actin filaments. Plays a role in the actin nucleation, actin filament bundle assembly, actin filament capping and severing. Binds phosphatidylinositol 4,5-bisphosphate (PIP2) and lysophosphatidic acid (LPA); binds LPA with higher affinity than PIP2. Binding to LPA increases its phosphorylation by SRC and inhibits all actin-modifying activities. Binding to PIP2 inhibits actin-capping and -severing activities but enhances actin-bundling activity. Regulates the intestinal epithelial cell morphology, cell invasion, cell migration and apoptosis. Protects against apoptosis induced by dextran sodium sulfate (DSS) in the gastrointestinal epithelium. Appears to regulate cell death by maintaining mitochondrial integrity. Enhances hepatocyte growth factor (HGF)-induced epithelial cell motility, chemotaxis and wound repair. Upon S.flexneri cell infection, its actin-severing activity enhances actin-based motility of the bacteria and plays a role during the dissemination. {ECO:0000269|PubMed:11500485, ECO:0000269|PubMed:14594952, ECO:0000269|PubMed:15084600, ECO:0000269|PubMed:15272027, ECO:0000269|PubMed:15342783, ECO:0000269|PubMed:16921170, ECO:0000269|PubMed:17182858, ECO:0000269|PubMed:17229814, ECO:0000269|PubMed:17606613, ECO:0000269|PubMed:18054784, ECO:0000269|PubMed:18198174, ECO:0000269|PubMed:19808673, ECO:0000269|PubMed:3087992}.;
- Disease
- DISEASE: Note=Biliary atresia is a chronic and progressive cholestatic liver disease of chilhood characterized by an abnormal villin gene expression and severe malformation of canalicular microvillus structure.;
- Pathway
- Regulation of Actin Cytoskeleton;IL2
(Consensus)
Recessive Scores
- pRec
- 0.358
Intolerance Scores
- loftool
- 0.796
- rvis_EVS
- 0.21
- rvis_percentile_EVS
- 67.54
Haploinsufficiency Scores
- pHI
- 0.339
- hipred
- Y
- hipred_score
- 0.542
- ghis
- 0.396
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.924
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vil1
- Phenotype
- normal phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- intestinal D-glucose absorption;apoptotic process;epidermal growth factor receptor signaling pathway;regulation of cell shape;response to bacterium;positive regulation of epithelial cell migration;actin filament polymerization;actin filament depolymerization;positive regulation of cell migration;positive regulation of actin filament depolymerization;epithelial cell differentiation;positive regulation of actin filament bundle assembly;regulation of microvillus length;cellular response to hepatocyte growth factor stimulus;positive regulation of multicellular organism growth;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;actin nucleation;actin filament severing;barbed-end actin filament capping;regulation of actin nucleation;actin filament capping;cytoplasmic actin-based contraction involved in cell motility;regulation of wound healing;protein-containing complex assembly;cellular response to epidermal growth factor stimulus;terminal web assembly;positive regulation of protein localization to plasma membrane;regulation of lamellipodium morphogenesis;positive regulation of lamellipodium morphogenesis
- Cellular component
- ruffle;cytoplasm;plasma membrane;microvillus;brush border;lamellipodium;filopodium;actin filament bundle;filopodium tip;extracellular exosome
- Molecular function
- calcium ion binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;lysophosphatidic acid binding;identical protein binding;protein homodimerization activity;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;actin filament binding