CPAP p.Thr424=
c.1272C>T · rs763888331 · VCV1902154
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 0.84 | GERP -3, phastCons 0.97 |
| Overall | ||
| CADD | 2.373 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
0.00676%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00522%
Overall
0.00328%
53/1,614,128 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| South Asian | 0.0121% | 8,279 |
| East Asian | 0.00891% | 11,218 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| European (non-Finnish) | 0.00263% | 38,065 |
| Admixed American | 0.00167% | 60,010 |
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.Thr424=
- Coding
- c.1272C>T
- MANE Select
- NM_018451
- dbSNP
- rs763888331
- Type
- single nucleotide variant
- Location
- chr13:24906766 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
Similar variants
- CPAP p.Thr424Ala 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
- 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-thr424 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown