PLAAT3 p.Pro86=
c.258G>A · VCV4871987
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0136%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.8 | GERP -4.8 |
| Overall | ||
| CADD | 1.959 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0136%
European (non-Finnish) · 161/1,180,030 alleles
Filtering AF
0.0119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.0112%
181/1,614,236 alleles · ultra-rare
exomes 161/1,461,872 · genomes 20/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0136% | 7,329 |
| Admixed American | 0.0133% | 7,505 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| African / African-American | 0.00533% | 18,767 |
| East Asian | 0.00223% | 44,884 |
| South Asian | 0.0022% | 45,543 |
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
- PLAAT3
- Protein
- p.Pro86=
- Coding
- c.258G>A
- MANE Select
- NM_001128203
- Type
- single nucleotide variant
- Location
- chr11:63590229 (GRCh38)
- Gene constraint
- LOEUF 1.838 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.12 · 7 PDB
- Residue 86
- an α-helix; the lrat domain
Similar variants
- PLAAT3 p.Pro86Leu Uncertain significance ★ same residue
- PLAAT3 p.Ser85Leu Uncertain significance ★★ ⚠ same type
- PLAAT3 c.387+2T>C Likely pathogenic ★ same type
- PLAAT3 c.16-3C>T Uncertain significance ★ same type
- PLAAT3 p.Ala125Thr Uncertain significance ★ ⚠ same type
- PLAAT3 p.Ala136Thr Uncertain significance ★ ⚠ same type
- PLAAT3 p.Ala137Pro Uncertain significance ★ ⚠ same type
- PLAAT3 p.Ala137Val 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/plaat3-p-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown