PIEZO2 p.Pro566=
c.1698T>C · rs11875564 · VCV261500
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 5.69%, afr) — too common for a highly-penetrant pathogenic allele
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 -12 | GERP -2.5 |
| Overall | ||
| CADD | 0.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.69%
African / African-American · 4,160/73,094 alleles
Filtering AF
5.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.49%
Overall
0.331%
5,082/1,536,620 alleles · common
exomes 2,565/1,384,294 · genomes 2,517/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.69% | 18 |
| Middle Eastern | 0.785% | 127 |
| Remaining individualsnot grpmax-eligible | 0.527% | 190 |
| Admixed American | 0.473% | 211 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0524% | 1,909 |
| European (non-Finnish) | 0.0248% | 4,038 |
| South Asian | 0.0215% | 4,653 |
| Finnishnot grpmax-eligible | 0.00219% | 45,664 |
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
- PIEZO2
- Protein
- p.Pro566=
- Coding
- c.1698T>C
- MANE Select
- NM_001378183
- dbSNP
- rs11875564
- Type
- single nucleotide variant
- Location
- chr18:10794832 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
Similar variants
- PIEZO2 c.1528-1G>A Likely pathogenic ★★ same type
- PIEZO2 c.4708+2T>G Likely pathogenic ★★ same type
- PIEZO2 c.5257-1G>A Pathogenic ★★ same type
- PIEZO2 c.7686+1G>C Likely pathogenic ★★ same type
- PIEZO2 p.Arg1600Ter Pathogenic/Likely pathogenic ★★ same type
- PIEZO2 p.Arg1743Ter Pathogenic/Likely pathogenic ★★ same type
- PIEZO2 p.Arg26Ter Likely pathogenic ★★ same type
- PIEZO2 p.Arg2799Cys 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/piezo2-p-pro566 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown