CADPS p.Ala69=
c.207G>A · rs543179326 · VCV786012
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.37%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 10.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.37%
African / African-American · 801/58,646 alleles
Filtering AF
1.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
0.0805%
853/1,059,400 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.37% | 73 |
| Middle Eastern | 0.0813% | 1,230 |
| Admixed American | 0.0783% | 1,277 |
| Remaining individualsnot grpmax-eligible | 0.0767% | 1,304 |
| East Asian | 0.0111% | 9,048 |
| European (non-Finnish) | 0.000692% | 144,493 |
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
- CADPS
- Protein
- p.Ala69=
- Coding
- c.207G>A
- MANE Select
- NM_003716
- dbSNP
- rs543179326
- Type
- single nucleotide variant
- Location
- chr3:62874823 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.13 · 1 PDB
- Residue 69
- the 'disordered' region
Similar variants
- CADPS p.Ser203= Benign ★★ same type
- CADPS p.Tyr579= Benign ★★ same type
- CAPS p.Arg18His Benign ★★ ⚠ same type
- CAPS p.Pro88Thr Benign ★★ ⚠ same type
- CADPS c.3477+2T>G Uncertain significance ★ same type
- CADPS p.Ala1047Thr Uncertain significance ★ ⚠ same type
- CADPS p.Ala1057Val Uncertain significance ★ ⚠ same type
- CADPS p.Ala1114Thr Uncertain significance ★ ⚠ same type
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/cadps-p-ala69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown