CFAP221 p.Ser529=
c.1587G>A · VCV4084038
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -7.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,862 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.0167%
270/1,613,592 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,486 |
| European (non-Finnish) | 0.021% | 4,758 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,499 |
| Admixed American | 0.00334% | 29,976 |
| African / African-American | 0.00267% | 37,428 |
| South Asian | 0.0022% | 45,505 |
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
- CFAP221
- Protein
- p.Ser529=
- Coding
- c.1587G>A
- MANE Select
- NM_001271049
- Type
- single nucleotide variant
- Location
- chr2:119627723 (GRCh38)
- Gene constraint
- LOEUF 1.102 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.53
Similar variants
- CFAP221 p.Arg131Ter Pathogenic ★ same type
- CFAP221 c.1025-1G>A Uncertain significance ★ same type
- CFAP221 p.Asn834Asp Uncertain significance ★ ⚠ same type
- CFAP221 p.Ile567Asn Uncertain significance ★ ⚠ same type
- CFAP221 p.Leu833Phe Uncertain significance ★ ⚠ same type
- CFAP221 c.1311+7A>G Likely benign ★ same type
- CFAP221 c.632-7C>G Likely benign ★ same type
- CFAP221 p.Arg433Cys Likely benign ★ 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/cfap221-p-ser529 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown