CFAP410 p.Pro87=
c.261G>A · rs1602079872 · VCV1159366
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000763%, nfe)
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 -6.6 | GERP -2.3 |
| Overall | ||
| CADD | 10.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000763%
European (non-Finnish) · 9/1,179,726 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000558%
9/1,612,188 alleles · very rare
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
- CFAP410
- Protein
- p.Pro87=
- Coding
- c.261G>A
- MANE Select
- NM_004928
- dbSNP
- rs1602079872
- Type
- single nucleotide variant
- Location
- chr21:44333145 (GRCh38)
- Gene constraint
- LOEUF 1.453 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.77 · 1 PDB
Similar variants
- CFAP410 p.Pro87Leu Uncertain significance ★★ ⚠ same residue
- CFAP410 p.Pro87Arg Uncertain significance ★ same residue
- CFAP410 c.545+1G>A Pathogenic ★★ same type
- CFAP410 c.642+2T>C Pathogenic ★★ same type
- CFAP410 c.643-1G>C Pathogenic ★★ same type
- CFAP410 c.643-23A>T Pathogenic/Likely pathogenic ★★ same type
- CFAP410 c.96+1G>A Pathogenic ★★ same type
- CFAP410 c.96+1G>T Pathogenic/Likely pathogenic ★★ 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/cfap410-p-pro87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown