PLIN3 p.Lys102=
c.306G>A · rs11552102 · VCV738945
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.542%, afr)
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 0.17 | GERP -1.4, phastCons 0.085 |
| Overall | ||
| CADD | 8.917 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.542%
African / African-American · 407/75,056 alleles
Filtering AF
0.499%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.482%
Overall
0.0298%
481/1,614,208 alleles · rare
exomes 250/1,461,880 · genomes 231/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.542% | 184 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| Admixed American | 0.0317% | 3,158 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.0022% | 45,386 |
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
- PLIN3
- Protein
- p.Lys102=
- Coding
- c.306G>A
- MANE Select
- NM_005817
- dbSNP
- rs11552102
- Type
- single nucleotide variant
- Location
- chr19:4859632 (GRCh38)
- Gene constraint
- LOEUF 1.213 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.04
Similar variants
- PLIN3 p.Ala139Thr Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala212Val Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala215Thr Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala371Ser Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala397Thr Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala397Val Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala62Thr Uncertain significance ★ ⚠ same type
- PLIN3 p.Ala72Val 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/plin3-p-lys102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown