Is PRICKLE1 p.Phe141= (c.423C>T) pathogenic?

PRICKLE1 p.Phe141= (c.423C>T) is classified Likely benign in PRICKLE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-29). Very rare (popmax 0.00668%, eas); Associated with epilepsy, progressive myoclonic, 1B.

What condition is associated with PRICKLE1 p.Phe141= (c.423C>T)?

PRICKLE1 p.Phe141= (c.423C>T) is associated with epilepsy, progressive myoclonic, 1B (ClinVar).

How common is PRICKLE1 p.Phe141= (c.423C>T) in the general population?

PRICKLE1 p.Phe141= (c.423C>T) is very rare (popmax 0.00668%, eas) (gnomAD).

PRICKLE1 p.Phe141=

c.423C>T · rs746728526 · VCV537250

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, 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	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.28	GERP -3.7, phastCons 0.001
Overall
CADD	6.946	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,892 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.00149% 24/1,614,020 alleles · very rare exomes 22/1,461,874 · genomes 2/152,146 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,964
South Asian	0.00549%	18,218
Admixed American	0.00333%	29,992
Remaining individualsnot grpmax-eligible	0.0016%	62,482
European (non-Finnish)	0.0011%	90,772

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.Phe141=
Coding: c.423C>T
MANE Select: NM_153026
dbSNP: rs746728526
Type: single nucleotide variant
Location: chr12:42468791 (GRCh38)
Gene constraint: LOEUF 0.279 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 55.55
Residue 141: the lim zinc-binding 1 domain

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 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
PRICKLE1 p.Ala506Thr 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-phe141 (accessed [today's date]).

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