CADPS2 p.Ala209=
c.627C>T · rs113324996 · VCV715005
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.444%, afr)
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 5 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.444%
African / African-American · 333/74,998 alleles
Filtering AF
0.405%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.389%
Overall
0.0234%
378/1,613,870 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.444% | 225 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.0267% | 3,750 |
| European (non-Finnish) | 8.48e-05% | 1,179,876 |
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
- CADPS2
- Protein
- p.Ala209=
- Coding
- c.627C>T
- MANE Select
- NM_017954
- dbSNP
- rs113324996
- Type
- single nucleotide variant
- Location
- chr7:122663396 (GRCh38)
- Gene constraint
- LOEUF 0.699 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.91
Similar variants
- CAPS2 p.Thr209Ala Likely benign ★ same residue
- CADPS2 c.3718-15A>C Benign ★★ same type
- CADPS2 p.Ala298Thr Benign ★★ same type
- CADPS2 p.Asp1088Asn Likely benign ★★ same type
- CADPS2 p.Glu1010Lys Benign ★★ same type
- CADPS2 p.Leu154= Likely benign ★★ same type
- CADPS2 p.Lys338= Benign ★★ same type
- CADPS2 p.Met828Val Benign ★★ ⚠ 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/cadps2-p-ala209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown