Is PGAM2 p.Gly108= (c.324G>A) pathogenic?

PGAM2 p.Gly108= (c.324G>A) is classified Benign in PGAM2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Common (popmax 9.46%, afr) — too common for a highly-penetrant pathogenic allele; Associated with glycogen storage disease due to phosphoglycerate mutase deficiency.

What condition is associated with PGAM2 p.Gly108= (c.324G>A)?

PGAM2 p.Gly108= (c.324G>A) is associated with glycogen storage disease due to phosphoglycerate mutase deficiency (ClinVar).

PGAM2 p.Gly108=

Q: How common is PGAM2 p.Gly108= (c.324G>A) in the general population?

PGAM2 p.Gly108= (c.324G>A) is common (popmax 9.46%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is Glycogen storage disease due to phosphoglycerate mutase deficiency inherited?

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

c.324G>A · rs112828964 · VCV360277

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 9.46%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

glycogen storage disease due to phosphoglycerate mutase deficiency

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 -4.3	GERP -3.7
Overall
CADD	0.824	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.46% African / African-American · 7,101/75,026 alleles

Filtering AF 9.28% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.21%

Overall 0.497% 8,019/1,614,048 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	9.46%	11
Remaining individualsnot grpmax-eligible	0.624%	160
Admixed American	0.543%	184
Middle Eastern	0.247%	404
European (non-Finnish)	0.0147%	6,821
South Asian	0.0143%	7,006
Finnishnot grpmax-eligible	0.00156%	63,928

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: PGAM2
Protein: p.Gly108=
Coding: c.324G>A
MANE Select: NM_001014436 · reported on NM_000290
dbSNP: rs112828964
Type: single nucleotide variant
Location: chr7:44065206 (GRCh38)

Full PGAM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease due to phosphoglycerate mutase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to phosphoglycerate mutase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Childhood

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/pgam2-p-gly108 (accessed [today's date]).

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