CFAP210 p.Leu493Pro
c.1478T>C · rs770025315 · VCV3143376
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00356%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.644 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 48 kb · p 0.24 · regional, not allelic |
| Overall | ||
| CADD | 25.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00356%
European (non-Finnish) · 42/1,179,880 alleles
Filtering AF
0.00267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00285%
46/1,613,850 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00356% | 28,092 |
| African / African-American | 0.00267% | 37,460 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,468 |
| South Asian | 0.0011% | 91,080 |
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
- CFAP210
- Protein
- p.Leu493Pro
- Coding
- c.1478T>C
- MANE Select
- NM_001085447
- dbSNP
- rs770025315
- Type
- single nucleotide variant
- Location
- chr2:169646022 (GRCh38)
- Structure
- AlphaFold pLDDT 81.20 · 2 PDB
Similar variants
- CFAP210 p.Ala196Thr Uncertain significance ★ same type
- CFAP210 p.Ala349Gly Uncertain significance ★ same type
- CFAP210 p.Ala372Gly Uncertain significance ★ same type
- CFAP210 p.Ala382Val Uncertain significance ★ same type
- CFAP210 p.Ala405Val Uncertain significance ★ same type
- CFAP210 p.Ala446Glu Uncertain significance ★ same type
- CFAP210 p.Ala462Thr Uncertain significance ★ same type
- CFAP210 p.Arg111His Uncertain significance ★ 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/cfap210-p-leu493pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown