PPP2CA p.Thr258=
c.774G>A · rs768863660 · VCV1583772
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -5.3 | GERP -3.8 |
| Overall | ||
| CADD | 6.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.0013%
21/1,613,886 alleles · ultra-rare
exomes 19/1,461,754 · genomes 2/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Admixed American | 0.005% | 19,999 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| African / African-American | 0.00133% | 74,910 |
| European (non-Finnish) | 0.0011% | 90,765 |
| South Asian | 0.0011% | 91,076 |
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
- PPP2CA
- Protein
- p.Thr258=
- Coding
- c.774G>A
- MANE Select
- NM_002715
- dbSNP
- rs768863660
- Type
- single nucleotide variant
- Location
- chr5:134199169 (GRCh38)
- Gene constraint
- LOEUF 0.315 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.86 · 50 PDB
- Residue 258
- a UniProt-annotated variant site (in hjs3; may be expressed at very low levels, if any); a UniProt-annotated variant site (in hjs3; loss of phosphatase activity in an in vitro assay; complete loss of interaction with pp2a subunit a ppp2r1a/ppp2r1b; interacts with alpha4/igbp1; loss of interaction with pp2a subunit b components); a β-strand
Similar variants
- PPP2CA p.Asp223His Pathogenic/Likely pathogenic ★★ same type
- PPP2CA p.Asp88Gly Pathogenic/Likely pathogenic ★★ same type
- PPP2CA p.Gln122His Likely pathogenic ★★ same type
- PPP2CA p.His191Arg Pathogenic/Likely pathogenic ★★ same type
- PPP2CA p.Tyr127Cys Likely pathogenic ★★ same type
- PPP2CA p.Tyr265Cys Likely pathogenic ★★ same type
- PPP2CA p.Arg108Cys Uncertain significance ★★ ⚠ same type
- PPP2CA p.Asp57Asn 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-thr258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown