P2RY2 p.Asp17=
c.51T>C · rs75314653 · VCV712083
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, 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 -2.1 | GERP -3.6 |
| Overall | ||
| CADD | 2.457 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
African / African-American · 945/74,982 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.17%
Overall
0.0639%
1,032/1,613,936 alleles · low-frequency
exomes 475/1,461,780 · genomes 557/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.26% | 79 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,453 |
| Admixed American | 0.0483% | 2,069 |
| Middle Eastern | 0.0165% | 6,060 |
| European (non-Finnish) | 0.0011% | 90,764 |
| South Asian | 0.0011% | 91,072 |
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
- P2RY2
- Protein
- p.Asp17=
- Coding
- c.51T>C
- MANE Select
- NM_002564
- dbSNP
- rs75314653
- Type
- single nucleotide variant
- Location
- chr11:73234210 (GRCh38)
- Gene constraint
- LOEUF 1.917 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 79.11 · 3 PDB
- Residue 17
- an α-helix
Similar variants
- P2RY2 p.Asp17Gly Likely benign ★ same residue
- P2RY2 p.Ala176Thr Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala252Thr Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala287Val Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala309Pro Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala80Thr Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala94Asp Uncertain significance ★ ⚠ same type
- P2RY2 p.Ala94Val 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/p2ry2-p-asp17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown