Is PPP2CA p.Glu19= (c.57G>A) pathogenic?

PPP2CA p.Glu19= (c.57G>A) is classified Likely benign in PPP2CA (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-23). Very rare (popmax 0.000424%, nfe).

How common is PPP2CA p.Glu19= (c.57G>A) in the general population?

PPP2CA p.Glu19= (c.57G>A) is very rare (popmax 0.000424%, nfe) (gnomAD).

PPP2CA p.Glu19=

c.57G>A · rs1296951642 · VCV1948072

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP 1.7, phastCons 1
Overall
CADD	18.97	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,179,224 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.00031% 5/1,610,848 alleles · very rare exomes 3/1,458,658 · genomes 2/152,190 · joint denominator

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.Glu19=
Coding: c.57G>A
MANE Select: NM_002715
dbSNP: rs1296951642
Type: single nucleotide variant
Location: chr5:134225805 (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-glu19 (accessed [today's date]).

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