CADPS2 p.Val799=
c.2397G>C · rs188401140 · VCV788646
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.958%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.502 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 0.16, phastCons 1 |
| Overall | ||
| CADD | 10.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.958%
Admixed American · 574/59,898 alleles
Filtering AF
0.893%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.868%
Overall
0.0647%
1,044/1,613,110 alleles · rare
exomes 921/1,460,872 · genomes 123/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.958% | 104 |
| East Asian | 0.796% | 126 |
| Remaining individualsnot grpmax-eligible | 0.0657% | 1,523 |
| South Asian | 0.0439% | 2,276 |
| African / African-American | 0.0173% | 5,769 |
| European (non-Finnish) | 0.00161% | 62,073 |
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.Val799=
- Coding
- c.2397G>C
- MANE Select
- NM_017954
- dbSNP
- rs188401140
- Type
- single nucleotide variant
- Location
- chr7:122438420 (GRCh38)
- Gene constraint
- LOEUF 0.699 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.91
- Residue 799
- the 'interaction with drd2' region
Similar variants
- CADPS2 p.Val799Leu 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-val799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown