Is GAA p.Pro425= (c.1275G>A) pathogenic?

GAA p.Pro425= (c.1275G>A) is classified Likely benign in GAA (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-29). Ultra-rare (popmax 0.0443%, sas); Associated with Cardiovascular phenotype.

What condition is associated with GAA p.Pro425= (c.1275G>A)?

GAA p.Pro425= (c.1275G>A) is associated with Cardiovascular phenotype, glycogen storage disease II (ClinVar).

How common is GAA p.Pro425= (c.1275G>A) in the general population?

GAA p.Pro425= (c.1275G>A) is ultra-rare (popmax 0.0443%, sas) (gnomAD).

GAA p.Pro425=

c.1275G>A · rs762826072 · VCV663382

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0443%, sas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -5.2	GERP -3.4
Overall
CADD	6.503	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0443% South Asian · 40/90,390 alleles

Filtering AF 0.0334% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0295%

Overall 0.00311% 50/1,608,884 alleles · ultra-rare exomes 45/1,456,630 · genomes 5/152,254 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0443%	2,260
African / African-American	0.00267%	37,478
European (non-Finnish)	0.000679%	147,270

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: GAA
Protein: p.Pro425=
Coding: c.1275G>A
MANE Select: NM_000152
dbSNP: rs762826072
Type: single nucleotide variant
Location: chr17:80108777 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.32 · 19 PDB
Residue 425: an α-helix

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: glycogen storage disease II

Similar variants

GAA p.Pro425Leu Uncertain significance ★★ ⚠ same residue
GAA p.Pro425Ser Uncertain significance ★★ ⚠ same residue
GAA p.Pro425Thr Uncertain significance ★ ⚠ same residue
GAA p.Pro425fs Pathogenic ★ same residue
GAA c.1076-1G>C Pathogenic ★★★ same condition
GAA c.1076-22T>G Pathogenic ★★★ same condition
GAA c.1194+5G>A Likely pathogenic ★★★ same condition
GAA c.1326+1G>A Pathogenic ★★★ same condition

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/gaa-p-pro425 (accessed [today's date]).

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