CFAP251 p.Pro659=
c.1977C>A · rs73415652 · VCV3057058
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 21.2%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
CFAP251-related disorder
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 -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.2%
African / African-American · 15,914/75,034 alleles
Filtering AF
20.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 20.8%
Overall
1.2%
19,398/1,614,106 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 21.2% | 5 |
| Remaining individualsnot grpmax-eligible | 1.58% | 63 |
| Admixed American | 1.39% | 72 |
| Middle Eastern | 1.29% | 78 |
| South Asian | 1.23% | 81 |
| European (non-Finnish) | 0.0389% | 2,571 |
| East Asian | 0.00891% | 11,221 |
| Finnishnot grpmax-eligible | 0.00469% | 21,344 |
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
- CFAP251
- Protein
- p.Pro659=
- Coding
- c.1977C>A
- MANE Select
- NM_144668
- dbSNP
- rs73415652
- Type
- single nucleotide variant
- Location
- chr12:121958518 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.84 · 1 PDB
- Residue 659
- a UniProt-annotated variant site (in spgf33)
Disease context
CFAP251-related disorder
Similar variants
- CFAP251 p.Arg267Ter Pathogenic ★★ same condition
- CFAP251 c.2492+10C>G Likely benign same condition
- CFAP251 p.Asn286= Benign same condition
- CFAP251 p.Asp511= Likely benign same condition
- CFAP251 p.Glu207= Likely benign same condition
- CFAP251 p.Gly649= Likely benign same condition
- CFAP251 p.His356= Benign same condition
- CFAP251 p.His740= Likely benign 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/cfap251-p-pro659 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown