AVIL
protein-codingadvillin, the group of Gelsolin/villins
Gene summary
The protein encoded by this gene is a member of the gelsolin/villin family of actin regulatory proteins. This protein has structural similarity to villin. It binds actin and may play a role in the development of neuronal cells that form ganglia. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0032826
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0032826
Submitter: ClinGen
AVIL – Nephrotic Syndrome Type 21 – Autosomal Recessive The AVIL gene is located on chromosome 12 at 12q14.1 and encodes the protein Advillin, a member of the gelsolin/villin family of actin-regulatory proteins. A mutation in AVIL was first reported in association with autosomal recessive nephrotic syndrome type 21 in 2017 (Rao et al., PMID: 29058690). Nephrotic syndrome type 21 (congenital nephrotic syndrome) is characterized by significant proteinuria during the first months or years of life, leading to generalized edema. AVIL-related nephrotic syndrome type 21 (OMIM: 618594) is currently the only disease association reported for this gene. This curation includes four variants (frameshift and missense) identified in three probands, all described in a single publication (Rao et al., PMID: 29058690). No additional evidence is available in the literature. (Genetic evidence: 3.1 points) The proposed mechanism of pathogenicity is loss of function. This gene-disease association is supported by expression studies and in vitro functional assays (PMID: 29058690). AVIL expression was demonstrated in extracts from cultured human podocytes (PMID: 29058690). Co-localization of AVIL and PLCE1 was observed in human podocytes transfected with GFP (green fluorescent protein)-tagged, full-length (FL) mouse Avil. The interaction between AVIL and PLCE1 was further confirmed in HEK293 cells. Functional studies showed that human podocytes transfected with three patient variants (Arg135Gln, Leu425Met, or Phe656Valfs*7) *exhibited reduced migration rates and impaired actin-binding and -bundling abilities. Additionally, EGF stimulation increased diacylglycerol (DAG) levels in control cells treated with scrambled siRNA. Knockdown of AVIL via siRNA decreased active DAG levels. This effect was rescued by overexpression of wild-type Avil, but not by any of the three patient-derived mutant clones (Arg135Gln, Leu425Met, and Phe656Valfs*7)*. A CRISPR-based AVIL knockdown model was also generated in zebrafish; however, the model did not exhibit a larval edema phenotype (Experimental Evidence: 2 points). Total Score: Genetic Evidence (3.1) + Experimental Evidence (2.0) = 5.1 points The AVIL-associated nephrotic syndrome type 21 is currently classified as ‘Limited’. This classification reflects the fact that the association has not yet been repeatedly demonstrated in both research and clinical diagnostic settings over time. This gene-disease relationship was initially evaluated by the ClinGen Glomerulopathy GCEP on June 27, 2023 (SOP Version 9), and re-evaluated on August 27, 2024 (SOP Version 10). The classification remained unchanged following the reevaluation.
Clinical Genomic Database (CGD)
Manifestation: Renal
Intervention: General
Rationale: 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
Comments: Renal transplant has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to AVIL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006576.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 19 | 3 | 23 | ||
| missense | 2 | 1 | 149 | 8 | 1 | 161 |
| nonsense | 3 | 3 | 6 | |||
| start loss | 0 | |||||
| frameshift | 2 | 2 | 4 | |||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 2 | 6 | 159 | 27 | 4 | 198 |
Highest pathogenic variant AF is 0.00020942772
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006567.3 | 19 | MANE Select | |
| Ensembl | ENSP00000449239.2 | 19 | MANE Select | |
| Ensembl | ENSP00000257861.3 | 19 | Standard | |
| Ensembl | ENSP00000450188.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cytoskeleton organization
- nervous system development
- positive regulation of neuron projection development
- actin filament capping
- cilium assembly
Molecular Function
- actin binding
- actin filament binding
Cellular Component
- cytoplasm
- actin cytoskeleton
- axon
- cell projection
- neuron projection
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000257861
- Coding exons
- 19
- Length
- 21329
- Individuals with no LoFs
- 125491
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 257
- Defined
- 125748
- p
- 0.00102
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.469 | 436 | 464 | 0.939 | 0.0000252 | 5400 |
| Missense (PolyPhen) | 164 | 182.06 | 0.90081 | 2160 | ||
| Synonymous | 0.00811 | 181 | 181 | 0.999 | 0.0000107 | 1555 |
| Loss of Function | 2.84 | 29 | 50.8 | 0.571 | 0.00000284 | 516 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0035 | 0.0035 | notable |
| Latino/Admixed American | 0.0018 | 0.0018 | notable |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00067 | 0.00066 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ca(2+)-regulated actin-binding protein. May have a unique function in the morphogenesis of neuronal cells which form ganglia. Required for SREC1-mediated regulation of neurite-like outgrowth. Plays a role in regenerative sensory axon outgrowth and remodeling processes after peripheral injury in neonates. Involved in the formation of long fine actin-containing filopodia-like structures in fibroblast. Plays a role in ciliogenesis. {ECO:0000269|PubMed:20393563}.;
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- LoFtool
- 0.956
- RVIS EVS
- -0.75
- RVIS percentile EVS
- 13.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.265
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |