Is PPP2CA p.Cys32Ser (c.95G>C) pathogenic?

PPP2CA p.Cys32Ser (c.95G>C) is classified Likely benign in PPP2CA (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-02). AlphaMissense: likely pathogenic (0.9099); Absent from gnomAD v4.1.

How common is PPP2CA p.Cys32Ser (c.95G>C) in the general population?

PPP2CA p.Cys32Ser (c.95G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PPP2CA p.Cys32Ser (c.95G>C)?

AlphaMissense predicts likely pathogenic (score 0.9099) — an in-silico prediction, not a clinical call.

PPP2CA p.Cys32Ser

c.95G>C · VCV4742752

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9099 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.9099	likely pathogenic
REVEL	0.455	indeterminate
SaProt	LLR -14.69	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.5	GERP 1.6, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 20 kb · p 0.0022 · regional, not allelic
Overall
CADD	29.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PPP2CA
Protein: p.Cys32Ser
Coding: c.95G>C
MANE Select: NM_002715
Type: single nucleotide variant
Location: chr5:134225767 (GRCh38)

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

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-cys32ser (accessed [today's date]).

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