CPAP p.Lys447Ter
c.1339A>T · rs797045447 · VCV210655
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Seckel syndrome 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CPAP
- Protein
- p.Lys447Ter
- Coding
- c.1339A>T
- MANE Select
- NM_018451
- dbSNP
- rs797045447
- Type
- single nucleotide variant
- Location
- chr13:24906699 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
- Residue 447
- the 'disordered' region
Similar variants
- 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.Ser529Ter Pathogenic/Likely pathogenic ★★ same condition
- CPAP c.444+3A>G Uncertain significance ★★ same condition
- CPAP p.Arg1023His Uncertain significance ★★ ⚠ same condition
- CPAP p.Arg535Trp Uncertain significance ★★ ⚠ 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-lys447ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown