PRKAG2 p.Phe293=
c.879C>T · rs193922697 · VCV2732758
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
2
cardiomyopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 0.86, phastCons 1 |
| Overall | ||
| CADD | 9.478 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,838 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000125%
2/1,605,772 alleles · very rare
exomes 2/1,453,524 · genomes 0/152,248 · joint denominator
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
- PRKAG2
- Protein
- p.Phe293=
- Coding
- c.879C>T
- MANE Select
- NM_016203
- dbSNP
- rs193922697
- Type
- single nucleotide variant
- Location
- chr7:151576438 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI 0.20 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.24
- Residue 293
- the cbs 1 domain
Similar variants
- PRKAG2 p.Phe293Leu Pathogenic/Likely pathogenic ★★ same residue
- 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 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-phe293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown