CFAP410 p.Pro174=
c.522G>A · rs372721170 · VCV1513809
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0268%, eas)
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 -5 | GERP -2.9 |
| Overall | ||
| CADD | 3.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0268%
East Asian · 12/44,804 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00192%
31/1,611,488 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0268% | 3,734 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,476 |
| Finnishnot grpmax-eligible | 0.00476% | 21,020 |
| African / African-American | 0.00401% | 24,964 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,556 |
| Admixed American | 0.00167% | 59,864 |
| European (non-Finnish) | 0.000509% | 196,603 |
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.Pro174=
- Coding
- c.522G>A
- MANE Select
- NM_004928
- dbSNP
- rs372721170
- Type
- single nucleotide variant
- Location
- chr21:44331866 (GRCh38)
- Gene constraint
- LOEUF 1.453 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.77 · 1 PDB
- Residue 174
- the 'disordered' region
Similar variants
- 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
- CFAP410 p.Gln119Ter 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-pro174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown