PRICKLE2 p.Lys290=
c.870A>G · VCV4963195
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00186%, nfe)
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 -1.7 | GERP -2.8 |
| Overall | ||
| CADD | 4.281 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00186%
European (non-Finnish) · 22/1,180,048 alleles
Filtering AF
0.00122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00136%
22/1,614,104 alleles · very rare
exomes 22/1,461,828 · genomes 0/152,276 · joint denominator
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.Lys290=
- Coding
- c.870A>G
- MANE Select
- NM_198859
- Type
- single nucleotide variant
- Location
- chr3:64147620 (GRCh38)
- Gene constraint
- LOEUF 0.34 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.41
- Residue 290
- the lim zinc-binding 3 domain
Similar variants
- PRICKLE2 c.*4330A>T Uncertain significance ★★ same type
- PRICKLE2 p.Ala143Thr Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala146Val Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala149Ser Uncertain significance ★★ same type
- PRICKLE2 p.Ala309Gly Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala33Ser Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala548Thr Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala650Val 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/prickle2-p-lys290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown