CFAP300 p.Ser123=
c.369T>C · rs372973997 · VCV1681458
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00628%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.137 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP 0.59, phastCons 0.97 |
| Overall | ||
| CADD | 9.476 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00628%
European (non-Finnish) · 74/1,178,954 alleles
Filtering AF
0.00511%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00509%
82/1,610,822 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00628% | 15,932 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,787 |
| Finnishnot grpmax-eligible | 0.00313% | 31,996 |
| Admixed American | 0.00168% | 59,480 |
| African / African-American | 0.00134% | 74,828 |
| South Asian | 0.00111% | 90,122 |
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.Ser123=
- Coding
- c.369T>C
- MANE Select
- NM_032930
- dbSNP
- rs372973997
- Type
- single nucleotide variant
- Location
- chr11:102066585 (GRCh38)
- Gene constraint
- LOEUF 1.386 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21
- Residue 123
- 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.Ser123Gly Uncertain significance ★ ⚠ 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-ser123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown