PPP2CA p.Val159del
c.473TGG[1] · rs2481051237 · VCV2108610
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.9, phastCons 1 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PPP2CA
- Protein
- p.Val159del
- Coding
- c.473TGG[1]
- MANE Select
- NM_002715
- dbSNP
- rs2481051237
- Type
- Microsatellite
- Location
- chr5:134201856 (GRCh38)
- Gene constraint
- LOEUF 0.315 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.86 · 50 PDB
- Residue 159
- a UniProt-annotated variant site (in hjs3; may be expressed at very low levels, if any); a β-strand
Similar variants
- PPP2CA p.Val159= Benign ★ same residue
- PPP2CA p.Tyr248_Asn249delinsTer Likely pathogenic ★ same type
- PPP2CA p.Tyr92del Likely pathogenic ★ same type
- PPP2CA p.Met1del 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/ppp2ca-p-val159del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown