CFAP251 p.Thr332=
c.996A>G · rs74462921 · VCV3043292
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.67%, eas)
Conditions
1
CFAP251-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.36 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.10 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -2 |
| Overall | ||
| CADD | 7.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.67%
East Asian · 1,645/44,850 alleles
Filtering AF
3.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.46%
Overall
0.114%
1,845/1,611,832 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.67% | 27 |
| Remaining individualsnot grpmax-eligible | 0.149% | 671 |
| South Asian | 0.0946% | 1,057 |
| Middle Eastern | 0.033% | 3,029 |
| Admixed American | 0.0117% | 8,562 |
| European (non-Finnish) | 0.00102% | 98,182 |
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.Thr332=
- Coding
- c.996A>G
- MANE Select
- NM_144668
- dbSNP
- rs74462921
- Type
- single nucleotide variant
- Location
- chr12:121934354 (GRCh38)
- Gene constraint
- LOEUF 0.829 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.84 · 1 PDB
- Residue 332
- 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-thr332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown