AVIL

advillin, the group of Gelsolin/villins

Basic information

Region (hg38): 12:57797375-57818734

Links

ENSG00000135407 ∙ NCBI:10677 ∙ OMIM:613397 ∙ HGNC:14188 ∙ Uniprot:O75366 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrotic syndrome, type 21 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 21	AR	General	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	Renal	29058690
Renal transplant has been described

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AVIL 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				9	2	11
missense		1	60	4	2	67
nonsense		1				1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			3	1	15	19
Total	0	2	65	14	19

Variants in AVIL

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

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

Position	Type	Phenotype	Significance	ClinVar
12-57797449-T-G		Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Uncertain significance (Jan 12, 2018)
12-57797478-A-G		Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Uncertain significance (Jan 13, 2018)
12-57797541-C-G		Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Benign (Jan 12, 2018)
12-57797580-G-C		Fatal mitochondrial disease due to combined oxidative phosphorylation defect type 3	Benign (Jan 13, 2018)
12-57797929-G-A			Uncertain significance (Mar 01, 2024)
12-57797930-C-T		AVIL-related disorder	Likely benign (Aug 06, 2022)
12-57799665-T-C			Benign (May 10, 2021)
12-57799799-T-A		not specified	Uncertain significance (Jun 18, 2024)
12-57799810-G-T		not specified	Uncertain significance (Oct 12, 2021)
12-57799819-C-G		not specified	Uncertain significance (Sep 20, 2023)
12-57799849-C-T		AVIL-related disorder	Likely benign (Dec 16, 2022)
12-57799859-A-G		not specified	Uncertain significance (Feb 16, 2023)
12-57799891-A-T		Nephrotic syndrome, type 21	Uncertain significance (Jul 18, 2022)
12-57799902-G-A		AVIL-related disorder	Likely benign (Dec 20, 2022)
12-57801169-G-C		not specified	Uncertain significance (Jul 26, 2022)
12-57801176-C-G		not specified	Uncertain significance (Dec 31, 2023)
12-57801221-A-G			Benign (Aug 20, 2018)
12-57801990-C-T			Benign (May 10, 2021)
12-57802018-T-C			Benign (May 10, 2021)
12-57802176-T-C		not specified	Uncertain significance (Sep 12, 2023)
12-57802274-C-T		AVIL-related disorder	Likely benign (May 25, 2022)
12-57802300-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-57802302-C-A		not specified	Uncertain significance (Jul 14, 2021)
12-57802302-C-G		not specified	Uncertain significance (Dec 12, 2023)
12-57802312-C-T		AVIL-related disorder	Uncertain significance (Feb 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AVIL	protein_coding	protein_coding	ENST00000257861	19	21329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-13	0.997	125491	0	257	125748	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.469	436	464	0.939	0.0000252	5400
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00533	0.00534
Ashkenazi Jewish	0.000204	0.000198
East Asian	0.000761	0.000761
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000666	0.000659
Middle Eastern	0.000761	0.000761
South Asian	0.00121	0.00121
Other	0.00131	0.00130

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.372
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.265

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Avil
• Phenotype: cellular 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail 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)

Gene ontology

• Biological process: cytoskeleton organization;nervous system development;positive regulation of neuron projection development;actin filament capping;cilium assembly
• Cellular component: cytoplasm;actin cytoskeleton;axon;cell projection;neuron projection
• Molecular function: actin binding;actin filament binding