PLA2G4A p.Phe243=
c.729T>C · VCV4740990
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00802%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | acceptor loss, 5 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 8.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00802%
African / African-American · 6/74,794 alleles
Filtering AF
0.00348%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.000373%
6/1,608,460 alleles · very rare
exomes 4/1,456,334 · genomes 2/152,126 · joint denominator
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
- PLA2G4A
- Protein
- p.Phe243=
- Coding
- c.729T>C
- MANE Select
- NM_024420
- Type
- single nucleotide variant
- Location
- chr1:186939041 (GRCh38)
- Gene constraint
- LOEUF 0.89 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 84.15 · 3 PDB
- Residue 243
- the pla2c domain; a turn
Similar variants
- PLA2G4A p.Ala34Thr Uncertain significance ★★ ⚠ same type
- PLA2G4A p.Ala364Thr Uncertain significance ★★ ⚠ same type
- PLA2G4A p.Met209Thr Uncertain significance ★★ ⚠ same type
- PLA2G4A p.Met468Val Uncertain significance ★★ ⚠ same type
- PLA2G4A p.Met470Val Uncertain significance ★★ ⚠ same type
- PLA2G4A p.Pro656Ser Uncertain significance ★★ ⚠ same type
- PLA2G4A c.115+13T>A Benign/Likely benign ★★ same type
- PLA2G4A c.115+7G>A Likely benign ★★ 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/pla2g4a-p-phe243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown