Is P2RY12 p.Ala3= (c.9C>T) pathogenic?

P2RY12 p.Ala3= (c.9C>T) is classified Likely benign in P2RY12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-24). Very rare (popmax 0.00892%, eas).

How common is P2RY12 p.Ala3= (c.9C>T) in the general population?

P2RY12 p.Ala3= (c.9C>T) is very rare (popmax 0.00892%, eas) (gnomAD).

P2RY12 p.Ala3=

c.9C>T · rs201192490 · VCV3022244

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00892%, eas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.6	GERP 2.2, phastCons 0.99
Overall
CADD	11.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00892% East Asian · 4/44,864 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.00105% 17/1,613,410 alleles · very rare exomes 15/1,461,322 · genomes 2/152,088 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00892%	11,216
African / African-American	0.00267%	37,471
South Asian	0.0011%	91,040
European (non-Finnish)	0.000848%	117,960

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: P2RY12
Protein: p.Ala3=
Coding: c.9C>T
MANE Select: NM_022788
dbSNP: rs201192490
Type: single nucleotide variant
Location: chr3:151338837 (GRCh38)

Full P2RY12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/p2ry12-p-ala3 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown