CPAP p.Pro411=
c.1233G>A · rs112133852 · VCV158191
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.2%, afr)
Conditions
2
Seckel syndrome 4
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 0.5 | GERP -3, phastCons 0.001 |
| Overall | ||
| CADD | 0.712 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.2%
African / African-American · 899/75,044 alleles
Filtering AF
1.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.11%
Overall
0.0711%
1,147/1,614,166 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.2% | 83 |
| Middle Eastern | 0.313% | 319 |
| Remaining individualsnot grpmax-eligible | 0.0832% | 1,202 |
| Admixed American | 0.0633% | 1,579 |
| European (non-Finnish) | 0.0115% | 8,677 |
| East Asian | 0.00446% | 22,442 |
| South Asian | 0.0011% | 91,078 |
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
- CPAP
- Protein
- p.Pro411=
- Coding
- c.1233G>A
- MANE Select
- NM_018451
- dbSNP
- rs112133852
- Type
- single nucleotide variant
- Location
- chr13:24906805 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 411
- the 'disordered' region
Similar variants
- CPAP p.Pro411Ser Uncertain significance ★★ ⚠ same residue
- CPAP p.Pro411Leu Uncertain significance ★ ⚠ same residue
- CPAP p.Arg1298Gln Likely pathogenic ★★ same condition
- CPAP p.Arg378Ter Pathogenic ★★ same condition
- CPAP p.Arg566Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP p.Gln657Ter Pathogenic/Likely pathogenic ★★ 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/cpap-p-pro411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown