AVIL

protein-coding

advillin, 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

NM_006576.4

Inheritance

AR

ClinVar variants

P:8U:159B:31

Top phenotype

Nephrotic syndrome, type 21

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr12:57,797,376-57,818,734

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~21.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

nephrotic syndrome, type 21LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0032826

Submitter: Labcorp Genetics (formerly Invitae)

nephrotic syndrome, type 21LIMITED

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)

Nephrotic syndrome, type 21AR

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

Refs: 29058690Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AVIL variants in ClinVar

7 Conditions Cataloged
not specifiedTotal: 147
Nephrotic syndrome, type 21Total: 22
AVIL-related disorderTotal: 22
not providedTotal: 16
Steroid-resistant nephrotic syndromeTotal: 4
TSFM-related disorderTotal: 1
Nephrotic syndromeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
19
clinvar
3
clinvar
23
missense
2
clinvar
1
clinvar
149
clinvar
8
clinvar
1
clinvar
161
nonsense
3
clinvar
3
clinvar
6
start loss
0
frameshift
2
clinvar
2
clinvar
4
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total26159274198

Highest pathogenic variant AF is 0.00020942772

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006576.4RefSeqNP_006567.319MANE Select
ENST00000549994.2EnsemblENSP00000449239.219MANE Select
ENST00000257861.7EnsemblENSP00000257861.319Standard
ENST00000549851.5EnsemblENSP00000450188.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4694364640.9390.00002525400
Missense (PolyPhen)164182.060.900812160
Synonymous0.008111811810.9990.00001071555
Loss of Function2.842950.80.5710.00000284516

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00350.0035notable
Latino/Admixed American0.00180.0018notable
Ashkenazi Jewish0.000200.00020rare
East Asian0.000760.00076rare
Finnish0.0000470.000046rare
European (Non-Finnish)0.000670.00066rare
South Asian0.00120.0012notable
Other0.00130.0013notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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