PPP1CB p.Val263=
c.789A>G · VCV3692601
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 0.2 | GERP -4.7, phastCons 0.19 |
| Overall | ||
| CADD | 11.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,870 alleles
Overall
0.000124%
2/1,614,124 alleles · very rare
exomes 2/1,461,776 · genomes 0/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,870 |
| European (non-Finnish) | 8.47e-05% | 1,179,972 |
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
- PPP1CB
- Protein
- p.Val263=
- Coding
- c.789A>G
- MANE Select
- NM_002709
- Type
- single nucleotide variant
- Location
- chr2:28793907 (GRCh38)
- Gene constraint
- LOEUF 0.247 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.91
Similar variants
- PPP1CB p.Ala56Pro Likely pathogenic ★★★ ⚠ same type
- PPP1CB p.Glu183Ala Pathogenic ★★★ ⚠ same type
- PPP1CB p.Glu183Val Pathogenic ★★★ same type
- PPP1CB p.Glu274Lys Likely pathogenic ★★★ same type
- PPP1CB p.Pro49Arg Pathogenic ★★★ same type
- PPP1CB c.53-9G>A Benign ★★★ same type
- PPP1CB p.Asp9= Benign ★★★ same type
- PPP1CB p.Gln67= Benign ★★★ 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/ppp1cb-p-val263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown