Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 13 submitters
gnomAD v4.1
Common
common (popmax 71.3%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
Seckel syndrome 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.295 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP 0.33, phastCons 1 |
| Overall | ||
| CADD | 9.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
71.3%
East Asian · 31,965/44,844 alleles
Filtering AF
70.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 70.4%
Overall
53.7%
865,353/1,610,908 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 71.3% | 1 |
| Admixed American | 62.4% | 2 |
| Finnishnot grpmax-eligible | 62.1% | 2 |
| European (non-Finnish) | 54.2% | 2 |
| Remaining individualsnot grpmax-eligible | 52.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 50.2% | 2 |
| South Asian | 49.6% | 2 |
| Middle Eastern | 47.6% | 2 |
| Amishnot grpmax-eligible | 31.1% | 3 |
| African / African-American | 29.2% | 3 |
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.Glu1014=
- Coding
- c.3042A>G
- MANE Select
- NM_018451
- dbSNP
- rs3742165
- Type
- single nucleotide variant
- Location
- chr13:24892817 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 1014
- the 'interaction with stil' region
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-glu1014 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown