P2RX2 p.Arg39=
c.115C>A · VCV3769091
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00154%, afr)
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 2.3 | phastCons 1 |
| Overall | ||
| CADD | 15.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00154%
African / African-American · 1/65,098 alleles
Filtering AF
3.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2e-05%
Overall
0.000227%
3/1,321,606 alleles · very rare
exomes 2/1,172,634 · genomes 1/148,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00154% | 65,098 |
| European (non-Finnish) | 0.000195% | 513,260 |
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.Arg39=
- Coding
- c.115C>A
- MANE Select
- NM_170682
- Type
- single nucleotide variant
- Location
- chr12:132618931 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.80 · 18 PDB
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-arg39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown