APOE p.Arg242=
c.726G>A · VCV3417793
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00196%, amr)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 5.718 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00196%
Admixed American · 1/51,092 alleles
Overall
0.000658%
1/152,074 alleles · very rare
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
- APOE
- Protein
- p.Arg242=
- Coding
- c.726G>A
- MANE Select
- NM_000041
- Type
- single nucleotide variant
- Location
- chr19:44909022 (GRCh38)
- Gene constraint
- LOEUF 1.319 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.13 · 31 PDB
- Residue 242
- the '8 x 22 aa approximate tandem repeats' region; the 'lipid-binding and lipoprotein association' region; a UniProt-annotated variant site (in hlpp3; apoe3 washington); a UniProt-annotated variant site (in apoe2 fukuoka)
Similar variants
- APOE p.Arg43Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- APOE p.Arg246Pro Uncertain significance ★★ same condition
- APOE p.Arg56His Uncertain significance ★★ ⚠ same condition
- APOE p.Gln119Pro Uncertain significance ★★ same condition
- APOE p.Gln181His Uncertain significance ★★ ⚠ same condition
- APOE p.Ser112Tyr Uncertain significance ★★ ⚠ same condition
- APOE p.Trp294Cys Uncertain significance ★★ ⚠ same condition
- APOE p.Val213Gly Uncertain significance ★★ ⚠ same condition
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/apoe-p-arg242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown