CPAP p.Pro233=
c.699G>A · rs587783413 · VCV158220
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
microcephaly 6, primary, autosomal recessive
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 0.33 | GERP -1.1 |
| Overall | ||
| CADD | 4.664 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.0018%
29/1,614,000 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| African / African-American | 0.012% | 8,322 |
| South Asian | 0.00768% | 13,013 |
| Admixed American | 0.00333% | 30,001 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| European (non-Finnish) | 0.000678% | 147,505 |
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.Pro233=
- Coding
- c.699G>A
- MANE Select
- NM_018451
- dbSNP
- rs587783413
- Type
- single nucleotide variant
- Location
- chr13:24909956 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
Similar variants
- 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
- CPAP p.Glu212Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP p.Glu955Ter 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-pro233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown