PLA2G3 p.Pro100=
c.300C>T · VCV4534215
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0336%, mid)
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 -1.9 | GERP -3.1 |
| Overall | ||
| CADD | 3.682 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0336%
Middle Eastern · 2/5,948 alleles
Filtering AF
0.00592%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00422%
Overall
0.0049%
79/1,613,408 alleles · ultra-rare
exomes 71/1,461,198 · genomes 8/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0336% | 2,974 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| European (non-Finnish) | 0.00576% | 17,353 |
| South Asian | 0.00439% | 22,770 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,228 |
| East Asian | 0.00223% | 44,894 |
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
- PLA2G3
- Protein
- p.Pro100=
- Coding
- c.300C>T
- MANE Select
- NM_015715
- Type
- single nucleotide variant
- Location
- chr22:31140055 (GRCh38)
- Gene constraint
- LOEUF 0.967 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.88
Similar variants
- PLA2G3 p.Ala252Thr Uncertain significance ★ ⚠ same type
- PLA2G3 p.Ala341Asp Uncertain significance ★ ⚠ same type
- PLA2G3 p.Ala388Val Uncertain significance ★ ⚠ same type
- PLA2G3 p.Ala446Thr Uncertain significance ★ ⚠ same type
- PLA2G3 p.Ala5Pro Uncertain significance ★ ⚠ same type
- PLA2G3 p.Ala88Asp Uncertain significance ★ ⚠ same type
- PLA2G3 p.Arg132Gln Uncertain significance ★ ⚠ same type
- PLA2G3 p.Arg182Gln 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/pla2g3-p-pro100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown