CFAP300 p.Cys103=
c.309C>T · rs143293029 · VCV1681457
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.232%, 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 0.4 | GERP -2.1, phastCons 0.99 |
| Overall | ||
| CADD | 8.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.232%
African / African-American · 174/74,926 alleles
Filtering AF
0.204%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.193%
Overall
0.0113%
182/1,610,612 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.232% | 431 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,780 |
| South Asian | 0.00444% | 22,523 |
| Admixed American | 0.00168% | 59,644 |
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.Cys103=
- Coding
- c.309C>T
- MANE Select
- NM_032930
- dbSNP
- rs143293029
- Type
- single nucleotide variant
- Location
- chr11:102066525 (GRCh38)
- Gene constraint
- LOEUF 1.386 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21
- Residue 103
- 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-cys103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown