PPARG p.Lys472=
c.1416G>A · rs770898588 · VCV728652
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.029%, eas)
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 12 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 12.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.029%
East Asian · 13/44,898 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.0013%
21/1,614,040 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.029% | 3,454 |
| African / African-American | 0.004% | 24,975 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000339% | 295,009 |
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
- PPARG
- Protein
- p.Lys472=
- Coding
- c.1416G>A
- MANE Select
- NM_138711
- dbSNP
- rs770898588
- Type
- single nucleotide variant
- Location
- chr3:12434133 (GRCh38)
- Gene constraint
- LOEUF 0.628 · pLI 0.21 (gnomAD)
- Structure
- AlphaFold pLDDT 76.11 · 321 PDB
- Residue 472
- the nr lbd domain; an α-helix
Similar variants
- PPARG p.Arg164Gln Likely pathogenic ★★ same type
- PPARG p.Arg395Cys Pathogenic/Likely pathogenic ★★ same type
- PPARG p.Arg395His Pathogenic/Likely pathogenic ★★ same type
- PPARG p.Pro465Leu Pathogenic/Likely pathogenic ★★ same type
- PPARG p.Tyr121Cys Pathogenic/Likely pathogenic ★★ same type
- PPARG c.-8A>G Uncertain significance ★★ ⚠ same type
- PPARG p.Arg110His Uncertain significance ★★ ⚠ same type
- PPARG p.Arg151Gln Uncertain significance ★★ ⚠ same type
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/pparg-p-lys472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown