Is PRKAG2 p.Ser86= (c.258C>T) pathogenic?

PRKAG2 p.Ser86= (c.258C>T) is classified Likely benign in PRKAG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-09). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with PRKAG2 p.Ser86= (c.258C>T)?

PRKAG2 p.Ser86= (c.258C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is PRKAG2 p.Ser86= (c.258C>T) in the general population?

PRKAG2 p.Ser86= (c.258C>T) is absent from gnomAD v4.1 (gnomAD).

PRKAG2 p.Ser86=

c.258C>T · rs2537923105 · VCV1793492

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

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 5.7	GERP 0.68, phastCons 1
Overall
CADD	11.02	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: PRKAG2
Protein: p.Ser86=
Coding: c.258C>T
MANE Select: NM_016203
dbSNP: rs2537923105
Type: single nucleotide variant
Location: chr7:151781360 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI 0.20 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.24
Residue 86: the 'disordered' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRKAG2 p.Arg302Gln Pathogenic ★★ same condition
PRKAG2 p.His530Arg Pathogenic ★★ same condition
PRKAG2 c.467-2A>G Uncertain significance ★★ same condition
PRKAG2 c.684+1G>A Uncertain significance ★★ same condition
PRKAG2 c.755-1G>A Uncertain significance ★★ same condition
PRKAG2 p.Ala229Val Uncertain significance ★★ ⚠ same condition
PRKAG2 p.Ala304Gly Uncertain significance ★★ ⚠ same condition
PRKAG2 p.Ala368Ser 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-ser86 (accessed [today's date]).

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