PLIN3 p.Ser196=
c.588G>A · rs149440810 · VCV723711
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.36%, afr)
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 -14 | GERP -5.3 |
| Overall | ||
| CADD | 1.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.36%
African / African-American · 1,019/74,996 alleles
Filtering AF
1.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
0.0804%
1,298/1,613,948 alleles · low-frequency
exomes 703/1,461,722 · genomes 595/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.36% | 74 |
| Middle Eastern | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.117% | 856 |
| Admixed American | 0.0667% | 1,500 |
| European (non-Finnish) | 0.0131% | 7,662 |
| South Asian | 0.00329% | 30,358 |
| East Asian | 0.00223% | 44,866 |
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.Ser196=
- Coding
- c.588G>A
- MANE Select
- NM_005817
- dbSNP
- rs149440810
- Type
- single nucleotide variant
- Location
- chr19:4852062 (GRCh38)
- Gene constraint
- LOEUF 1.213 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.04
Similar variants
- PLIN3 p.Lys102= Benign ★★ same type
- 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
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-ser196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown