CPAP p.Lys972=
c.2916G>A · rs752228607 · VCV3034444
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0428%, sas)
Conditions
1
CENPJ-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.038 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.94, phastCons 1 |
| Overall | ||
| CADD | 6.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0428%
South Asian · 39/91,060 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0284%
Overall
0.00242%
39/1,613,694 alleles · ultra-rare
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.Lys972=
- Coding
- c.2916G>A
- MANE Select
- NM_018451
- dbSNP
- rs752228607
- Type
- single nucleotide variant
- Location
- chr13:24899494 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 972
- the 'interaction with stil' region
Disease context
CENPJ-related disorder
Similar variants
- CPAP c.2693-2A>G Likely pathogenic ★★ same condition
- CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP p.Gln1027Ter Likely pathogenic ★ same condition
- CPAP p.Gln345Ter Likely pathogenic ★ same condition
- CPAP p.Glu230Ter Likely pathogenic ★ same condition
- CPAP c.*9A>C Uncertain significance same condition
- CPAP p.Leu188= Likely benign same condition
- CPAP p.Thr1187= Likely benign 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-lys972 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown