CFAP410 p.Pro116=
c.348G>A · VCV3608437
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -11 | GERP -2.9 |
| Overall | ||
| CADD | 0.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,036 alleles
Filtering AF
0.000432%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000315%
Overall
0.000813%
13/1,599,106 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,036 |
| East Asian | 0.00225% | 44,398 |
| South Asian | 0.00111% | 90,102 |
| European (non-Finnish) | 0.000854% | 117,055 |
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.Pro116=
- Coding
- c.348G>A
- MANE Select
- NM_004928
- Type
- single nucleotide variant
- Location
- chr21:44333058 (GRCh38)
- Gene constraint
- LOEUF 1.453 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.77 · 1 PDB
- Residue 116
- a UniProt-annotated variant site (in smdax); the lrrct domain
Similar variants
- CFAP410 p.Pro116Leu Pathogenic/Likely pathogenic ★★ 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
- CFAP410 p.Arg73Pro 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-pro116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown