VIL1

villin 1, the group of Gelsolin/villins

Basic information

Region (hg38): 2:218419120-218453295

Previous symbols: [ "VIL" ]

Links

ENSG00000127831 ∙ NCBI:7429 ∙ OMIM:193040 ∙ HGNC:12690 ∙ Uniprot:P09327 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VIL1 gene.

• Inborn genetic diseases (33 variants)
• not provided (5 variants)
• not specified (1 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.

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	1
missense			34	1	3	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	4

Variants in VIL1

This is a list of pathogenic ClinVar variants found in the VIL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-218423792-G-T		not specified	Uncertain significance (Apr 10, 2023)
2-218423794-G-A		VIL1-related disorder	Likely benign (Jul 12, 2019)
2-218423861-C-G		VIL1-related disorder	Likely benign (Sep 18, 2019)
2-218424305-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-218424329-G-A		VIL1-related disorder	Benign (Aug 21, 2019)
2-218425647-C-A		not specified	Uncertain significance (Feb 06, 2024)
2-218425738-C-T		VIL1-related disorder	Benign (Jun 11, 2019)
2-218425739-G-A		not specified	Uncertain significance (Nov 14, 2023)
2-218425760-T-C		not specified	Uncertain significance (Apr 13, 2022)
2-218427969-C-T		not specified	Uncertain significance (Aug 23, 2021)
2-218427978-G-T		not specified	Uncertain significance (Jun 02, 2023)
2-218428036-T-C		not specified	Uncertain significance (Aug 28, 2021)
2-218428255-G-A		not specified	Uncertain significance (Dec 02, 2021)
2-218428263-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-218428286-G-T		not specified	Uncertain significance (Apr 25, 2022)
2-218429282-C-T		VIL1-related disorder	Likely benign (Jul 12, 2019)
2-218429310-G-A		not specified	Uncertain significance (Feb 11, 2022)
2-218429316-A-G		not specified	Uncertain significance (Jun 27, 2022)
2-218429322-G-A		not specified	Uncertain significance (Aug 17, 2021)
2-218429376-C-G		not specified	Uncertain significance (Nov 04, 2023)
2-218429376-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-218429399-C-T		not specified	Uncertain significance (Nov 30, 2022)
2-218429401-C-A		not specified	Likely benign (Mar 15, 2018)
2-218429435-G-A		not specified	Uncertain significance (May 18, 2023)
2-218429441-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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