CPAP p.Asp1196=
c.3588C>T · VCV4753150
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.90 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -3.7 |
| Overall | ||
| CADD | 0.528 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
South Asian · 19/91,068 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00198%
32/1,614,064 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,793 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.000593% | 168,569 |
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.Asp1196=
- Coding
- c.3588C>T
- MANE Select
- NM_018451
- Type
- single nucleotide variant
- Location
- chr13:24884353 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 1196
- the 'interaction with stil' region
Similar variants
- CPAP p.Asp1196Asn Pathogenic same residue
- CPAP c.2693-2A>G Likely pathogenic ★★ same type
- CPAP p.Arg1298Gln Likely pathogenic ★★ same type
- CPAP p.Arg378Ter Pathogenic ★★ same type
- CPAP p.Arg566Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Arg902Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ 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/cpap-p-asp1196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown