PPP1CB p.Ala258=
c.774T>C · rs1254598326 · VCV1760458
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Cardiovascular phenotype
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 2.4 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 17.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,880 alleles
Overall
0.000124%
2/1,613,890 alleles · very rare
exomes 0/1,461,666 · genomes 2/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,880 |
| South Asian | 0.0011% | 91,056 |
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.Ala258=
- Coding
- c.774T>C
- MANE Select
- NM_002709
- dbSNP
- rs1254598326
- Type
- single nucleotide variant
- Location
- chr2:28793892 (GRCh38)
- Gene constraint
- LOEUF 0.247 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.91
Similar variants
- PPP1CB p.Ala2Val Uncertain significance ★★ ⚠ same condition
- PPP1CB p.Leu11Val Uncertain significance ★★ ⚠ same condition
- PPP1CB p.Leu6Val Uncertain significance ★★ ⚠ same condition
- PPP1CB p.Phe234Leu Uncertain significance ★★ ⚠ same condition
- PPP1CB p.Ser99Cys Uncertain significance ★★ ⚠ same condition
- PPP1CB p.Ala127= Likely benign ★★ same condition
- PPP1CB p.Ala228= Likely benign ★★ same condition
- PPP1CB p.Ala278= Likely benign ★★ 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/ppp1cb-p-ala258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown