PRICKLE2 p.Lys837=
c.2511G>A · rs1474159913 · VCV749436
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.96, phastCons 1 |
| Overall | ||
| CADD | 16.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,022 alleles
Overall
6.19e-05%
1/1,614,212 alleles · very rare
exomes 1/1,461,892 · genomes 0/152,320 · 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.Lys837=
- Coding
- c.2511G>A
- MANE Select
- NM_198859
- dbSNP
- rs1474159913
- Type
- single nucleotide variant
- Location
- chr3:64099075 (GRCh38)
- Gene constraint
- LOEUF 0.34 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.41
- Residue 837
- the 'disordered' region
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-lys837 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown