PLA2G5 p.Pro99=
c.297C>T · rs139841773 · VCV1121697
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, afr)
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 -20 | GERP -3.6 |
| Overall | ||
| CADD | 0.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
African / African-American · 37/75,030 alleles
Filtering AF
0.0368%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0323%
Overall
0.00254%
41/1,614,106 alleles · ultra-rare
exomes 17/1,461,842 · genomes 24/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0493% | 2,028 |
| European (non-Finnish) | 0.000339% | 294,992 |
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
- PLA2G5
- Protein
- p.Pro99=
- Coding
- c.297C>T
- MANE Select
- NM_000929
- dbSNP
- rs139841773
- Type
- single nucleotide variant
- Location
- chr1:20090572 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.19 · 1 PDB
Similar variants
- PLA2G5 p.Pro99Ser Uncertain significance ★ ⚠ same residue
- PLA2G5 p.Arg112Trp Uncertain significance ★★ ⚠ same type
- PLA2G5 p.Arg53Gln Uncertain significance ★★ ⚠ same type
- PLA2G5 p.Arg53Ter Uncertain significance ★★ same type
- PLA2G5 p.Asn134Lys Uncertain significance ★★ ⚠ same type
- PLA2G5 p.Cys103Arg Uncertain significance ★★ ⚠ same type
- PLA2G5 p.Cys103Ter Uncertain significance ★★ same type
- PLA2G5 p.Glu98Lys 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/pla2g5-p-pro99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown