Is PRKAG2 p.Ser87= (c.261C>T) pathogenic?

PRKAG2 p.Ser87= (c.261C>T) is classified Likely benign in PRKAG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-19). No allele count reported in gnomAD v4.1 (AN 1,613,674); Associated with lethal congenital glycogen storage disease of heart.

What condition is associated with PRKAG2 p.Ser87= (c.261C>T)?

PRKAG2 p.Ser87= (c.261C>T) is associated with lethal congenital glycogen storage disease of heart (ClinVar).

How common is PRKAG2 p.Ser87= (c.261C>T) in the general population?

PRKAG2 p.Ser87= (c.261C>T) is no allele count reported in gnomAD v4.1 (AN 1,613,674) (gnomAD).

PRKAG2 p.Ser87=

Q: How is Fatal congenital hypertrophic cardiomyopathy due to glycogen storage disease inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

c.261C>T · rs1377817526 · VCV1591551

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,674)

Conditions

lethal congenital glycogen storage disease of heart

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 5.6	GERP -0.74, phastCons 1
Overall
CADD	10.55	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,674). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRKAG2
Protein: p.Ser87=
Coding: c.261C>T
MANE Select: NM_016203
dbSNP: rs1377817526
Type: single nucleotide variant
Location: chr7:151781357 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI 0.20 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.24
Residue 87: the 'disordered' region

Full PRKAG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lethal congenital glycogen storage disease of heart — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Fatal congenital hypertrophic cardiomyopathy due to glycogen storage disease (Orphanet):

Inheritance: Not applicable
Onset: Antenatal, Neonatal

Similar variants

PRKAG2 p.Arg302Gln Pathogenic ★★ same condition
PRKAG2 p.Arg302Pro Pathogenic/Likely pathogenic ★★ same condition
PRKAG2 p.Arg531Gln Pathogenic ★★ same condition
PRKAG2 p.His530Arg Pathogenic ★★ same condition
PRKAG2 p.Phe293Leu Pathogenic/Likely pathogenic ★★ same condition
PRKAG2 c.1005+6T>C Uncertain significance ★★ same condition
PRKAG2 c.1006-3C>T Uncertain significance ★★ same condition
PRKAG2 c.1052-6A>G Uncertain significance ★★ 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/prkag2-p-ser87 (accessed [today's date]).

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