Is PGAM2 p.Cys153= (c.459C>T) pathogenic?

PGAM2 p.Cys153= (c.459C>T) is classified Conflicting classifications of pathogenicity in PGAM2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-06-01). Rare (popmax 0.169%, nfe); Associated with glycogen storage disease due to phosphoglycerate mutase deficiency.

What condition is associated with PGAM2 p.Cys153= (c.459C>T)?

PGAM2 p.Cys153= (c.459C>T) is associated with glycogen storage disease due to phosphoglycerate mutase deficiency (ClinVar).

How common is PGAM2 p.Cys153= (c.459C>T) in the general population?

PGAM2 p.Cys153= (c.459C>T) is rare (popmax 0.169%, nfe) (gnomAD).

PGAM2 p.Cys153=

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.459C>T · rs143809043 · VCV360272

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.169%, nfe)

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 -8.9	GERP -3.7
Overall
CADD	1.671	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.169% European (non-Finnish) · 1,994/1,179,606 alleles

Filtering AF 0.163% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.16%

Overall 0.133% 2,134/1,607,600 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.169%	592
Remaining individualsnot grpmax-eligible	0.0929%	1,077
Admixed American	0.0735%	1,361
Middle Eastern	0.0496%	2,017
African / African-American	0.024%	4,168
Finnishnot grpmax-eligible	0.0223%	4,494
Ashkenazi Jewishnot grpmax-eligible	0.0135%	7,385

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.Cys153=
Coding: c.459C>T
MANE Select: NM_001014436 · reported on NM_000290
dbSNP: rs143809043
Type: single nucleotide variant
Location: chr7:44064968 (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-cys153 (accessed [today's date]).

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