CFAP300 p.Lys59=
c.177G>A · rs2496303494 · VCV2095494
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 4.1 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 12.22 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CFAP300
- Protein
- p.Lys59=
- Coding
- c.177G>A
- MANE Select
- NM_032930
- dbSNP
- rs2496303494
- Type
- single nucleotide variant
- Location
- chr11:102047881 (GRCh38)
- Gene constraint
- LOEUF 1.386 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21
- Residue 59
- a UniProt-annotated variant site (in cild38; loss of ciliary axoneme inner dynein arm and outer dynein arm structures in patient respiratory epithelial cells)
Similar variants
- CFAP300 p.Lys59Ter Likely pathogenic same residue
- CFAP300 p.Arg121Ter Pathogenic ★★ same type
- CFAP300 p.Arg144Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP300 p.Gln160Ter Pathogenic ★★ same type
- CFAP300 p.Gln52Ter Pathogenic ★★ same type
- CFAP300 p.His259Arg Pathogenic/Likely pathogenic ★★ same type
- CFAP300 c.110+16A>G Benign ★★ same type
- CFAP300 c.192+59A>C Benign ★★ 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/cfap300-p-lys59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown