PERCC1 p.Pro15=
c.45C>T · rs185485996 · VCV3250540
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.996%, 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 -0.88 | GERP -2.5 |
| Overall | ||
| CADD | 3.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.996%
Middle Eastern · 16/1,606 alleles
Filtering AF
0.625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.511%
Overall
0.377%
1,507/399,794 alleles · rare
exomes 1,043/247,484 · genomes 464/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.996% | 100 |
| European (non-Finnish) | 0.547% | 183 |
| Remaining individualsnot grpmax-eligible | 0.453% | 221 |
| South Asian | 0.359% | 279 |
| Admixed American | 0.246% | 406 |
| Ashkenazi Jewishnot grpmax-eligible | 0.244% | 410 |
| African / African-American | 0.08% | 1,250 |
| Finnishnot grpmax-eligible | 0.041% | 2,438 |
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.Pro15=
- Coding
- c.45C>T
- MANE Select
- NM_001365310
- dbSNP
- rs185485996
- Type
- single nucleotide variant
- Location
- chr16:1432638 (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.Pro221= 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-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown