Is PGAM2 p.Ala242= (c.726C>T) pathogenic?

PGAM2 p.Ala242= (c.726C>T) is classified Conflicting classifications of pathogenicity in PGAM2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-04-01). Rare (popmax 0.354%, afr); Associated with glycogen storage disease due to phosphoglycerate mutase deficiency.

What condition is associated with PGAM2 p.Ala242= (c.726C>T)?

PGAM2 p.Ala242= (c.726C>T) is associated with glycogen storage disease due to phosphoglycerate mutase deficiency (ClinVar).

How common is PGAM2 p.Ala242= (c.726C>T) in the general population?

PGAM2 p.Ala242= (c.726C>T) is rare (popmax 0.354%, afr) (gnomAD).

PGAM2 p.Ala242=

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.726C>T · rs142209394 · VCV360270

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.354%, afr)

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 3.8	GERP -1, phastCons 1
Overall
CADD	9.659	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.354% African / African-American · 266/75,054 alleles

Filtering AF 0.319% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.306%

Overall 0.0216% 348/1,614,210 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.354%	282
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0384%	2,604
Admixed American	0.0383%	2,610
European (non-Finnish)	0.00263%	38,066
South Asian	0.0011%	91,088

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.Ala242=
Coding: c.726C>T
MANE Select: NM_001014436 · reported on NM_000290
dbSNP: rs142209394
Type: single nucleotide variant
Location: chr7:44062800 (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-ala242 (accessed [today's date]).

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