AVIL p.Gln413=
c.1239A>G · rs148660762 · VCV3041006
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.268%, afr)
Conditions
1
AVIL-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | donor loss, 2 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.11 | GERP -0.97, phastCons 0.018 |
| Overall | ||
| CADD | 4.495 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.268%
African / African-American · 201/75,076 alleles
Filtering AF
0.237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.226%
Overall
0.0137%
221/1,614,146 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.268% | 374 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.005% | 20,008 |
| South Asian | 0.0022% | 45,543 |
| European (non-Finnish) | 0.000508% | 196,676 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- AVIL
- Protein
- p.Gln413=
- Coding
- c.1239A>G
- MANE Select
- NM_006576
- dbSNP
- rs148660762
- Type
- single nucleotide variant
- Location
- chr12:57807683 (GRCh38)
- Gene constraint
- LOEUF 0.81 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.82 · 1 PDB
- Residue 413
- the 'core' region
Disease context
AVIL-related disorder
Similar variants
- AVIL p.Glu667Lys Uncertain significance ⚠ same condition
- AVIL c.1818-6T>C Likely benign same condition
- AVIL p.Gly299Arg Likely benign same condition
- AVIL p.Gly434= Likely benign same condition
- AVIL p.Leu679= Likely benign same condition
- AVIL p.Leu747Phe Likely benign same condition
- AVIL p.Leu764= Likely benign same condition
- AVIL p.Val29= Likely benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/avil-p-gln413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown