P2RX2 p.Asp326=
c.978C>T · rs762231212 · VCV680394
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.86 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9 | |
| Overall | ||
| CADD | 0.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/60,012 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00576%
93/1,613,924 alleles · ultra-rare
exomes 83/1,461,750 · genomes 10/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,751 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,619 |
| European (non-Finnish) | 0.00585% | 17,101 |
| South Asian | 0.00329% | 30,361 |
| African / African-American | 0.00133% | 74,924 |
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
- P2RX2
- Protein
- p.Asp326=
- Coding
- c.978C>T
- MANE Select
- NM_170682
- dbSNP
- rs762231212
- Type
- single nucleotide variant
- Location
- chr12:132621327 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.80 · 18 PDB
- Residue 326
- the 'pore-forming motif' region
Similar variants
- P2RX2 c.174-1G>A Uncertain significance ★★ same type
- P2RX2 p.Arg218His Uncertain significance ★★ ⚠ same type
- P2RX2 p.Arg286Gln Uncertain significance ★★ ⚠ same type
- P2RX2 p.Arg302Thr Uncertain significance ★★ ⚠ same type
- P2RX2 p.Arg315Cys Uncertain significance ★★ ⚠ same type
- P2RX2 p.Arg315His Uncertain significance ★★ ⚠ same type
- P2RX2 p.Arg324Cys Uncertain significance ★★ ⚠ same type
- P2RX2 p.Asp180Asn Uncertain significance ★★ ⚠ 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/p2rx2-p-asp326 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown