PERCC1 p.Pro221=
c.663G>A · VCV3257121
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.114%, sas)
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 -1.7 | GERP -2.8 |
| Overall | ||
| CADD | 2.808 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.114%
South Asian · 9/7,866 alleles
Filtering AF
0.0596%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0445%
Overall
0.00527%
21/398,832 alleles · rare
exomes 14/246,516 · genomes 7/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.114% | 874 |
| African / African-American | 0.0041% | 24,375 |
| East Asian | 0.00356% | 28,082 |
| European (non-Finnish) | 0.00354% | 28,270 |
| Finnishnot grpmax-eligible | 0.00317% | 31,550 |
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
- PERCC1
- Protein
- p.Pro221=
- Coding
- c.663G>A
- MANE Select
- NM_001365310
- Type
- single nucleotide variant
- Location
- chr16:1433256 (GRCh38)
- Structure
- AlphaFold pLDDT 64.66
Similar variants
- PERCC1 p.Tyr116Ter Likely pathogenic ★★ same type
- PERCC1 p.Ser63Ter Likely pathogenic ★ same type
- PERCC1 p.Tyr130Ter Pathogenic ★ same type
- PERCC1 p.Gly181Arg Uncertain significance ★ ⚠ same type
- PERCC1 p.Arg58Gln Likely benign ★ same type
- PERCC1 p.Pro15= 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/percc1-p-pro221 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown