PLIN1 p.Val402=
c.1206G>A · rs756116966 · VCV3051345
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.168%, sas)
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 0.52 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 5.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.168%
South Asian · 153/91,068 alleles
Filtering AF
0.146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.138%
Overall
0.0113%
182/1,613,978 alleles · rare
exomes 175/1,461,652 · genomes 7/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.168% | 595 |
| Middle Eastern | 0.0165% | 6,054 |
| East Asian | 0.00891% | 11,219 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| European (non-Finnish) | 0.00161% | 62,102 |
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
- PLIN1
- Protein
- p.Val402=
- Coding
- c.1206G>A
- MANE Select
- NM_002666
- dbSNP
- rs756116966
- Type
- single nucleotide variant
- Location
- chr15:89666939 (GRCh38)
- Gene constraint
- LOEUF 1.201 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.52
Similar variants
- PLIN1 p.Val402Met Uncertain significance ★ ⚠ same residue
- PLIN1 p.Val402fs Pathogenic same residue
- PLIN1 p.Ala361Glu Uncertain significance ★★ ⚠ same type
- PLIN1 p.Arg125Cys Uncertain significance ★★ ⚠ same type
- PLIN1 p.Glu151Lys Uncertain significance ★★ ⚠ same type
- PLIN1 p.Leu404Phe Uncertain significance ★★ ⚠ same type
- PLIN1 p.Leu90Pro Uncertain significance ★★ ⚠ same type
- PLIN1 p.Thr345Ala 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/plin1-p-val402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown