Is P2RX2 c.314del pathogenic?

P2RX2 c.314del is classified Uncertain significance in P2RX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-02). Very rare (popmax 0.00173%, amr).

How common is P2RX2 c.314del in the general population?

P2RX2 c.314del is very rare (popmax 0.00173%, amr) (gnomAD).

P2RX2 c.314del

rs763300549 · VCV2578064

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00173%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00173% Admixed American · 1/57,920 alleles

Overall 0.000188% 3/1,592,978 alleles · very rare exomes 2/1,441,452 · genomes 1/151,526 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.00354%	28,224
Admixed Americangrpmax	0.00173%	57,920
European (non-Finnish)	8.55e-05%	1,169,727

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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
Coding: c.314del
MANE Select: NM_170682 · reported on NM_174873
dbSNP: rs763300549
Type: Deletion
Location: chr12:132619678 (GRCh38)
Gene constraint: LOEUF 1.276 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.80 · 18 PDB

Full P2RX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

P2RX2 c.635+2_635+5del Uncertain significance ★★ same type
P2RX2 p.Glu71_Ser76del Uncertain significance ★★ same type
P2RX2 c.173+25_173+31del Likely benign ★★ same type
P2RX2 c.775-74_775-14del Benign/Likely benign ★★ same type
P2RX2 p.Ile441_Ser442insTer Benign/Likely benign ★★ same type
P2RX2 c.173+11_173+31del Uncertain significance ★ same type
P2RX2 c.453_457+26del Uncertain significance ★ same type
P2RX2 c.635+1del 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-c-314del (accessed [today's date]).

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