Is G6PC1 p.Pro293= (c.879A>C) pathogenic?

G6PC1 p.Pro293= (c.879A>C) is classified Likely benign in G6PC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-24). Absent from gnomAD v4.1; Associated with glycogen storage disease due to glucose-6-phosphatase deficiency type IA.

What condition is associated with G6PC1 p.Pro293= (c.879A>C)?

G6PC1 p.Pro293= (c.879A>C) is associated with glycogen storage disease due to glucose-6-phosphatase deficiency type IA (ClinVar).

How common is G6PC1 p.Pro293= (c.879A>C) in the general population?

G6PC1 p.Pro293= (c.879A>C) is absent from gnomAD v4.1 (gnomAD).

G6PC1 p.Pro293=

Q: How is Glycogen storage disease due to glucose-6-phosphatase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.879A>C · VCV4727840

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

glycogen storage disease due to glucose-6-phosphatase deficiency type IA

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 -20	GERP -3.9
Overall
CADD	0.035	PHRED · no single calibrated threshold — expert panels disagree

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: G6PC1
Protein: p.Pro293=
Coding: c.879A>C
MANE Select: NM_000151
Type: single nucleotide variant
Location: chr17:42911231 (GRCh38)
Gene constraint: LOEUF 0.963 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.21 · 6 PDB
Residue 293: an α-helix

Full G6PC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease due to glucose-6-phosphatase deficiency type IA — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to glucose-6-phosphatase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

G6PC1 c.230+1G>C Pathogenic/Likely pathogenic ★★ same condition
G6PC1 c.231-1G>A Pathogenic ★★ same condition
G6PC1 c.447-1G>C Likely pathogenic ★★ same condition
G6PC1 c.563-3C>G Pathogenic/Likely pathogenic ★★ same condition
G6PC1 p.Ala124Thr Pathogenic/Likely pathogenic ★★ same condition
G6PC1 p.Ala274Thr Likely pathogenic ★★ same condition
G6PC1 p.Ala274Val Pathogenic/Likely pathogenic ★★ same condition
G6PC1 p.Ala65Pro Pathogenic/Likely 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/g6pc1-p-pro293 (accessed [today's date]).

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