P2RX2 p.Ala14=
c.42C>T · rs376966028 · VCV737628
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.324%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.007 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -3.8 |
| Overall | ||
| CADD | 7.344 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.324%
African / African-American · 215/66,334 alleles
Filtering AF
0.289%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.275%
Overall
0.0167%
229/1,370,152 alleles · rare
exomes 101/1,219,486 · genomes 128/150,666 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.324% | 309 |
| Remaining individualsnot grpmax-eligible | 0.0181% | 5,537 |
| Admixed American | 0.00873% | 11,457 |
| European (non-Finnish) | 0.00019% | 527,632 |
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.Ala14=
- Coding
- c.42C>T
- MANE Select
- NM_170682
- dbSNP
- rs376966028
- Type
- single nucleotide variant
- Location
- chr12:132618858 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.80 · 18 PDB
Similar variants
- P2RX2 p.Ala14Pro Uncertain significance ★ ⚠ same residue
- P2RX2 p.Ala14Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown