PRICKLE1 p.Ser770=
c.2310C>T · rs529575327 · VCV512527
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -4 | GERP -3.7 |
| Overall | ||
| CADD | 2.626 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,868 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.00062%
10/1,614,024 alleles · very rare
exomes 8/1,461,880 · genomes 2/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,434 |
| South Asian | 0.0022% | 45,539 |
| European (non-Finnish) | 0.000508% | 196,667 |
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.Ser770=
- Coding
- c.2310C>T
- MANE Select
- NM_153026
- dbSNP
- rs529575327
- Type
- single nucleotide variant
- Location
- chr12:42459995 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.55
- Residue 770
- the 'disordered' region
Similar variants
- PRICKLE1 c.1639+4C>T Uncertain significance ★★ same type
- PRICKLE1 c.384+6C>A Uncertain significance ★★ same type
- PRICKLE1 p.Ala142Thr Uncertain significance ★★ ⚠ same type
- PRICKLE1 p.Ala145Val Uncertain significance ★★ ⚠ same type
- PRICKLE1 p.Ala34Thr Uncertain significance ★★ ⚠ same type
- PRICKLE1 p.Ala34Val Uncertain significance ★★ ⚠ same type
- PRICKLE1 p.Ala492Thr Uncertain significance ★★ ⚠ same type
- PRICKLE1 p.Ala506Thr 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/prickle1-p-ser770 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown