CPAP p.Ala1072=
c.3216G>A · rs138755582 · VCV1481349
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.222 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.66 | donor loss at this position · masked 0 · deltas |
| Pangolin | Δ0.41 | loss · gain 0.26 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 21.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,980 alleles
Filtering AF
0.00207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00183%
Overall
0.00229%
37/1,613,620 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,980 |
| European (non-Finnish) | 0.00288% | 34,696 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,494 |
| African / African-American | 0.00133% | 75,002 |
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.Ala1072=
- Coding
- c.3216G>A
- MANE Select
- NM_018451
- dbSNP
- rs138755582
- Type
- single nucleotide variant
- Location
- chr13:24892643 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 1072
- the 'interaction with stil' region
Similar variants
- CPAP p.Ala1072Glu Uncertain significance ★ ⚠ same residue
- CPAP p.Ala1072Val Uncertain significance ★ ⚠ 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
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-ala1072 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown