P2RY1 p.Val262=
c.786A>G · VCV4684732
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 68.4%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.32 | donor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.091 | GERP -3.3, phastCons 0.7 |
| Overall | ||
| CADD | 6.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
68.4%
African / African-American · 51,247/74,926 alleles
Filtering AF
67.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 67.7%
Overall
18.6%
299,603/1,613,912 alleles · common
exomes 252,456/1,461,818 · genomes 47,147/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 68.4% | 1 |
| East Asian | 28.9% | 3 |
| Amishnot grpmax-eligible | 26.6% | 4 |
| Admixed American | 23.7% | 4 |
| Middle Eastern | 21.7% | 5 |
| Remaining individualsnot grpmax-eligible | 20.5% | 5 |
| South Asian | 18.8% | 5 |
| European (non-Finnish) | 14.9% | 7 |
| Finnishnot grpmax-eligible | 14.7% | 7 |
| Ashkenazi Jewishnot grpmax-eligible | 13.9% | 7 |
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
- P2RY1
- Protein
- p.Val262=
- Coding
- c.786A>G
- MANE Select
- NM_002563
- Type
- single nucleotide variant
- Location
- chr3:152836568 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.12 · 5 PDB
- Residue 262
- an α-helix
Similar variants
- P2RY1 p.Ala147Gly Uncertain significance ★ ⚠ same type
- P2RY1 p.Ala270Thr Uncertain significance ★ ⚠ same type
- P2RY1 p.Arg149Gln Uncertain significance ★ ⚠ same type
- P2RY1 p.Arg287Trp Uncertain significance ★ ⚠ same type
- P2RY1 p.Asn113Ser Uncertain significance ★ ⚠ same type
- P2RY1 p.Asp208Glu Uncertain significance ★ ⚠ same type
- P2RY1 p.Asp289Tyr Uncertain significance ★ ⚠ same type
- P2RY1 p.Gln291Ter 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/p2ry1-p-val262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown