PRKAG2 p.Ser3=
c.9C>T · rs771101951 · VCV2021073
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,609,068)
Conditions
4
Cardiovascular phenotype
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 6.9 | GERP 2.9, phastCons 1 |
| Overall | ||
| CADD | 14.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,609,068). 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.Ser3=
- Coding
- c.9C>T
- MANE Select
- NM_016203
- dbSNP
- rs771101951
- Type
- single nucleotide variant
- Location
- chr7:151876612 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI 0.20 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.24
- Residue 3
- the 'disordered' region
Similar variants
- PRKAG2 p.Ser3Asn Uncertain significance ★★ same residue
- PRKAG2 p.Ser3Arg Uncertain significance ★ ⚠ same residue
- PRKAG2 p.Arg302Gln Pathogenic ★★ same condition
- PRKAG2 p.Arg302Pro Pathogenic/Likely pathogenic ★★ same condition
- PRKAG2 p.Arg531Gln Pathogenic ★★ same condition
- PRKAG2 p.Glu506Gln Likely pathogenic ★★ same condition
- PRKAG2 p.His530Arg Pathogenic ★★ same condition
- PRKAG2 p.Phe293Leu Pathogenic/Likely pathogenic ★★ 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-ser3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown