PLIN5 p.Val22=
c.66G>A · VCV3905481
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0325%, 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 -0.49 | GERP -1.8 |
| Overall | ||
| CADD | 6.894 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0325%
South Asian · 27/83,084 alleles
Filtering AF
0.0229%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00245%
38/1,550,290 alleles · ultra-rare
exomes 36/1,397,978 · genomes 2/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0325% | 3,077 |
| East Asian | 0.00238% | 41,994 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,998 |
| European (non-Finnish) | 0.000784% | 127,477 |
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
- PLIN5
- Protein
- p.Val22=
- Coding
- c.66G>A
- MANE Select
- NM_001013706
- Type
- single nucleotide variant
- Location
- chr19:4531817 (GRCh38)
- Gene constraint
- LOEUF 1.525 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.54
- Residue 22
- the 'essential for lipid droplet targeting' region; the 'interaction with lipe' region
Similar variants
- PLIN5 p.Val22Met Uncertain significance ★ ⚠ same residue
- PLIN5 p.Pro452Leu Uncertain significance ★★ ⚠ same type
- PLIN5 p.Ala174Val Uncertain significance ★ ⚠ same type
- PLIN5 p.Ala175Pro Uncertain significance ★ ⚠ same type
- PLIN5 p.Ala232Thr Uncertain significance ★ ⚠ same type
- PLIN5 p.Ala232Val Uncertain significance ★ ⚠ same type
- PLIN5 p.Ala310Thr Uncertain significance ★ ⚠ same type
- PLIN5 p.Ala341Val 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/plin5-p-val22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown