Is P2RY13 p.Pro188= (c.564A>G) pathogenic?

P2RY13 p.Pro188= (c.564A>G) is classified Likely benign in P2RY13 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-01). Rare (popmax 0.25%, eas).

How common is P2RY13 p.Pro188= (c.564A>G) in the general population?

P2RY13 p.Pro188= (c.564A>G) is rare (popmax 0.25%, eas) (gnomAD).

P2RY13 p.Pro188=

c.564A>G · VCV3778523

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.25%, eas)

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 -14	GERP -4
Overall
CADD	0.445	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.25% East Asian · 112/44,876 alleles

Filtering AF 0.212% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.198%

Overall 0.00712% 115/1,614,034 alleles · rare exomes 109/1,461,762 · genomes 6/152,272 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.25%	401
Remaining individualsnot grpmax-eligible	0.0032%	31,251
European (non-Finnish)	8.47e-05%	1,179,960

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: P2RY13
Protein: p.Pro188=
Coding: c.564A>G
MANE Select: NM_176894
Type: single nucleotide variant
Location: chr3:151328492 (GRCh38)
Gene constraint: LOEUF 1.133 · pLI 0.61 (gnomAD)
Structure: AlphaFold pLDDT 83.33 · 1 PDB

Full P2RY13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

P2RY13 p.Ala65Val Uncertain significance ★ ⚠ same type
P2RY13 p.Arg117Cys Uncertain significance ★ ⚠ same type
P2RY13 p.Arg240Thr Uncertain significance ★ ⚠ same type
P2RY13 p.Arg334Thr Uncertain significance ★ ⚠ same type
P2RY13 p.Asn84His Uncertain significance ★ same type
P2RY13 p.Asp246His Uncertain significance ★ ⚠ same type
P2RY13 p.Cys311Tyr Uncertain significance ★ ⚠ same type
P2RY13 p.Gln332His 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/p2ry13-p-pro188 (accessed [today's date]).

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