PIEZO2 p.Cys7=
c.21C>T · rs1378314458 · VCV1963545
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00734%, 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 0.25 | GERP -1.3, phastCons 0.55 |
| Overall | ||
| CADD | 12.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00734%
East Asian · 3/40,878 alleles
Filtering AF
0.00195%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000195%
3/1,537,118 alleles · very rare
exomes 3/1,384,864 · genomes 0/152,254 · joint denominator
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.Cys7=
- Coding
- c.21C>T
- MANE Select
- NM_001378183
- dbSNP
- rs1378314458
- Type
- single nucleotide variant
- Location
- chr18:11148568 (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-cys7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown