Is PRICKLE1 p.Pro802= (c.2406A>G) pathogenic?

PRICKLE1 p.Pro802= (c.2406A>G) is classified Likely benign in PRICKLE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-06). Very rare (popmax 0.00669%, eas); Associated with epilepsy, progressive myoclonic, 1B.

What condition is associated with PRICKLE1 p.Pro802= (c.2406A>G)?

PRICKLE1 p.Pro802= (c.2406A>G) is associated with epilepsy, progressive myoclonic, 1B (ClinVar).

How common is PRICKLE1 p.Pro802= (c.2406A>G) in the general population?

PRICKLE1 p.Pro802= (c.2406A>G) is very rare (popmax 0.00669%, eas) (gnomAD).

PRICKLE1 p.Pro802=

c.2406A>G · rs377290931 · VCV2163705

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00669%, eas)

Conditions

epilepsy, progressive myoclonic, 1B

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 -3.5	GERP -3.7
Overall
CADD	0.185	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00669% East Asian · 3/44,874 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.000434% 7/1,614,154 alleles · very rare exomes 7/1,461,888 · genomes 0/152,266 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00669%	14,958
Remaining individualsnot grpmax-eligible	0.0032%	31,252
Admixed American	0.00167%	60,008
African / African-American	0.00133%	75,038

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: PRICKLE1
Protein: p.Pro802=
Coding: c.2406A>G
MANE Select: NM_153026
dbSNP: rs377290931
Type: single nucleotide variant
Location: chr12:42459899 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 55.55
Residue 802: the 'disordered' region

Full PRICKLE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epilepsy, progressive myoclonic, 1B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRICKLE1 p.Pro802Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
PRICKLE1 c.1639+4C>T Uncertain significance ★★ same condition
PRICKLE1 c.384+6C>A Uncertain significance ★★ same condition
PRICKLE1 p.Ala142Thr Uncertain significance ★★ ⚠ same condition
PRICKLE1 p.Ala145Val Uncertain significance ★★ ⚠ same condition
PRICKLE1 p.Ala34Thr Uncertain significance ★★ ⚠ same condition
PRICKLE1 p.Ala34Val Uncertain significance ★★ ⚠ same condition
PRICKLE1 p.Ala492Thr 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/prickle1-p-pro802 (accessed [today's date]).

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