CAV3 p.Ala102=
c.306G>A · rs149375325 · VCV46535
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0613%, afr)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -5.9 |
| Overall | ||
| CADD | 5.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0613%
African / African-American · 46/75,048 alleles
Filtering AF
0.0471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.00589%
95/1,614,182 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0613% | 1,631 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,935 |
| South Asian | 0.00768% | 13,013 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| Admixed American | 0.00333% | 30,016 |
| European (non-Finnish) | 0.00254% | 39,335 |
| Finnishnot grpmax-eligible | 0.00156% | 64,006 |
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
- CAV3
- Protein
- p.Ala102=
- Coding
- c.306G>A
- MANE Select
- NM_033337
- dbSNP
- rs149375325
- Type
- single nucleotide variant
- Location
- chr3:8745717 (GRCh38)
- Gene constraint
- LOEUF 1.064 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 88.54
- Residue 102
- the 'required for interaction with dag1' region
Similar variants
- CAV3 p.Ala102Val Uncertain significance ★★ ⚠ same residue
- CAV3 c.114+2T>C Pathogenic ★★ same condition
- CAV3 p.Ala46Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CAV3 p.Arg27Gln Pathogenic ★★ same condition
- CAV3 p.Trp71Ter Pathogenic/Likely pathogenic ★★ same condition
- CAV3 c.114+5G>C Uncertain significance ★★ same condition
- CAV3 p.Ala134Glu Uncertain significance ★★ ⚠ same condition
- CAV3 p.Ala134Pro Uncertain significance ★★ ⚠ 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/cav3-p-ala102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown