CFAP300 p.Ser56=
c.168C>T · rs73593065 · VCV1681449
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.76%, afr)
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 0.097 | GERP -2.5, phastCons 0.94 |
| Overall | ||
| CADD | 8.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.76%
African / African-American · 2,073/75,054 alleles
Filtering AF
2.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.62%
Overall
0.15%
2,426/1,614,200 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.76% | 36 |
| Middle Eastern | 0.379% | 264 |
| Admixed American | 0.232% | 432 |
| Remaining individualsnot grpmax-eligible | 0.187% | 534 |
| European (non-Finnish) | 0.00593% | 16,857 |
| South Asian | 0.00439% | 22,770 |
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
- CFAP300
- Protein
- p.Ser56=
- Coding
- c.168C>T
- MANE Select
- NM_032930
- dbSNP
- rs73593065
- Type
- single nucleotide variant
- Location
- chr11:102047872 (GRCh38)
- Gene constraint
- LOEUF 1.386 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21
- Residue 56
- 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.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
- CFAP300 c.268+13T>C Benign/Likely 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-ser56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown