Is PRICKLE2 p.Val2= (c.6G>A) pathogenic?

PRICKLE2 p.Val2= (c.6G>A) is classified Benign in PRICKLE2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-03). Rare (popmax 0.193%, sas); Associated with Progressive myoclonic epilepsy type 5.

What condition is associated with PRICKLE2 p.Val2= (c.6G>A)?

PRICKLE2 p.Val2= (c.6G>A) is associated with Progressive myoclonic epilepsy type 5 (ClinVar).

How common is PRICKLE2 p.Val2= (c.6G>A) in the general population?

PRICKLE2 p.Val2= (c.6G>A) is rare (popmax 0.193%, sas) (gnomAD).

PRICKLE2 p.Val2=

c.6G>A · rs201779407 · VCV750610

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.193%, sas)

Conditions

Progressive myoclonic epilepsy type 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.19	GERP -2.5, phastCons 0.96
Overall
CADD	16.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.193% South Asian · 176/91,088 alleles

Filtering AF 0.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.161%

Overall 0.0128% 206/1,614,160 alleles · rare exomes 188/1,461,838 · genomes 18/152,322 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.193%	518
Remaining individualsnot grpmax-eligible	0.0384%	2,604
East Asian	0.00223%	44,872
African / African-American	0.00133%	75,060
European (non-Finnish)	0.000339%	295,010

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: PRICKLE2
Protein: p.Val2=
Coding: c.6G>A
MANE Select: NM_198859
dbSNP: rs201779407
Type: single nucleotide variant
Location: chr3:64198922 (GRCh38)
Gene constraint: LOEUF 0.34 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 56.41

Full PRICKLE2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Progressive myoclonic epilepsy type 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRICKLE2 p.Ala143Thr Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala146Val Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala149Ser Uncertain significance ★★ same condition
PRICKLE2 p.Ala309Gly Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala33Ser Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala548Thr Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala650Val Uncertain significance ★★ ⚠ same condition
PRICKLE2 p.Ala707Thr Uncertain significance ★★ ⚠ same condition

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/prickle2-p-val2 (accessed [today's date]).

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