Is PPP2CA p.Phe308del (c.922_924del) pathogenic?

PPP2CA p.Phe308del (c.922924del) is classified Uncertain significance in PPP2CA (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with prostate cancer.

What condition is associated with PPP2CA p.Phe308del (c.922_924del)?

PPP2CA p.Phe308del (c.922_924del) is associated with prostate cancer (ClinVar).

How common is PPP2CA p.Phe308del (c.922_924del) in the general population?

PPP2CA p.Phe308del (c.922_924del) is no gnomAD frequency available for this variant (gnomAD).

PPP2CA p.Phe308del

c.922_924del · rs864622012 · VCV219302

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

prostate cancer

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 12	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.Phe308del
Coding: c.922_924del
MANE Select: NM_002715
dbSNP: rs864622012
Type: Deletion
Location: chr5:134197778 (GRCh38)
Gene constraint: LOEUF 0.315 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 94.86 · 50 PDB
Residue 308: 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 UniProt-annotated variant site (in hjs3; almost complete loss of phosphatase activity in an in vitro assay; decreased interaction with pp2a subunit a ppp2r1a/ppp2r1b; strongly decreased interaction with pp2a subunit b components ppp2r2a and ppp2r3a; increased interaction with pp2a subunit b component strn3; no effect on interaction with pp2a subunit b components ppp2r5a, ppp2r5b, ppp2r5c, ppp2r5d and ppp2r5e); a turn

Full PPP2CA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

prostate cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PPP2CA p.Phe308dup Likely pathogenic ★ same residue
PPP2CA p.Cys133_Leu134insTer Pathogenic ★ same type
PPP2CA p.Gln125fs Likely pathogenic ★ same type
PPP2CA p.Gln187fs Pathogenic ★ same type
PPP2CA p.Glu25fs Pathogenic ★ same type
PPP2CA p.Phe164fs Likely pathogenic ★ same type
PPP2CA p.Tyr127fs Pathogenic ★ same type
PPP2CA c.313-7_313-5del Likely 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/ppp2ca-p-phe308del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown