APOE — 243 ClinVar variants

All ClinVar germline APOE variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 131 flagged for review →

11 Pathogenic · 1 Pathogenic/Likely pathogenic · 7 Likely pathogenic · 13 Conflicting · 3 Benign · 1 Benign/Likely benign · 93 Likely benign · 114 Uncertain significance

Full APOE gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 131

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 8

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 6

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 50

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 67

The independent predictors disagree with each other — read with care.

All APOE variants

Pathogenic 11

  • p.Leu167del Multiple submitters Cardiovascular phenotype
  • c.237-2A>G No assertion criteria hyperlipoproteinemia type 3
  • p.Arg152Gln No assertion criteria APOE2 VARIANT ⚠
  • p.Arg163Pro No assertion criteria lipoprotein glomerulopathy
  • p.Arg246Cys No assertion criteria APOE2-DUNEDIN ⚠
  • p.Arg292His No assertion criteria APOE4 VARIANT ⚠
  • p.Glu139_Gly145dup No assertion criteria hyperlipoproteinemia type 3
  • p.Glu21Lys No assertion criteria HYPERLIPOPROTEINEMIA, TYPE III, AND ATHEROSCLEROSIS ASSOCIATED WITH APOE5 ⚠
  • p.Gly49fs No assertion criteria hyperlipoproteinemia type 3
  • p.Lys164Gln No assertion criteria Hyperlipoproteinemia, type III, due to APOE2 ⚠
  • p.Lys164Glu No assertion criteria hyperlipoproteinemia type 3 ⚠

Pathogenic/Likely pathogenic 1

  • p.Arg43Cys Multiple submitters age related macular degeneration 1 ⚠

Likely pathogenic 7

Conflicting classifications of pathogenicity 13

Benign 3

Benign/Likely benign 1

  • p.Ala217= Multiple submitters hyperlipoproteinemia type 3

Likely benign 93

  • c.237-16_237-13del Multiple submitters familial hypercholesterolemia
  • p.Ala23= Multiple submitters Cardiovascular phenotype
  • p.Arg209= Multiple submitters Cardiovascular phenotype
  • p.Asp83= Multiple submitters Alzheimer disease 3
  • p.Glu127= Multiple submitters Cardiovascular phenotype
  • p.Glu249= Multiple submitters Cardiovascular phenotype
  • p.Pro30= Multiple submitters Cardiovascular phenotype
  • p.Ser314= Multiple submitters Cardiovascular phenotype
  • p.Ser40= Multiple submitters Cardiovascular phenotype
  • p.Val213= Multiple submitters Cardiovascular phenotype
  • c.-23-280C>T Single submitter
  • c.*25C>T Single submitter familial hypercholesterolemia
  • p.Ala104= Single submitter Cardiovascular phenotype
  • p.Ala118= Single submitter Cardiovascular phenotype
  • p.Ala124= Single submitter Cardiovascular phenotype
  • p.Ala182= Single submitter Cardiovascular phenotype
  • p.Ala184= Single submitter Cardiovascular phenotype
  • p.Ala18Thr Single submitter Cardiovascular phenotype
  • p.Ala234= Single submitter Cardiovascular phenotype
  • p.Ala255= Single submitter Cardiovascular phenotype
  • p.Ala304= Single submitter Cardiovascular phenotype
  • p.Ala309= Single submitter Cardiovascular phenotype
  • p.Ala310= Single submitter Cardiovascular phenotype
  • p.Ala7= Single submitter Cardiovascular phenotype
  • p.Ala80= Single submitter Cardiovascular phenotype
  • p.Arg108Gln Single submitter Cardiovascular phenotype ⚠
  • p.Arg152= Single submitter Cardiovascular phenotype
  • p.Arg154= Single submitter Cardiovascular phenotype
  • p.Arg163= Single submitter Cardiovascular phenotype
  • p.Arg185= Single submitter Cardiovascular phenotype
  • p.Arg190= Single submitter Cardiovascular phenotype
  • p.Arg196= Single submitter Cardiovascular phenotype
  • p.Arg207= Single submitter Cardiovascular phenotype
  • p.Arg224= Single submitter Cardiovascular phenotype
  • p.Arg231= Single submitter Cardiovascular phenotype
  • p.Arg233= Single submitter Cardiovascular phenotype
  • p.Arg235= Single submitter Cardiovascular phenotype
  • p.Arg242= Single submitter Cardiovascular phenotype
  • p.Arg258= Single submitter Cardiovascular phenotype
  • p.Arg33His Single submitter Cardiovascular phenotype
  • p.Asp128= Single submitter Cardiovascular phenotype
  • p.Asp171= Single submitter Cardiovascular phenotype
  • p.Asp248Glu Single submitter Cardiovascular phenotype
  • p.Asp315= Single submitter Cardiovascular phenotype
  • p.Gln135= Single submitter Cardiovascular phenotype
  • p.Gln205= Single submitter Cardiovascular phenotype
  • p.Glu197= Single submitter Cardiovascular phenotype
  • p.Glu21= Single submitter Cardiovascular phenotype
  • p.Glu262= Single submitter Cardiovascular phenotype
  • p.Glu263= Single submitter Cardiovascular phenotype
  • p.Glu29= Single submitter Cardiovascular phenotype
  • p.Glu299= Single submitter Cardiovascular phenotype
  • p.Gly138= Single submitter Cardiovascular phenotype
  • p.Gly214= Single submitter Cardiovascular phenotype
  • p.His158= Single submitter Cardiovascular phenotype
  • p.Ile268= Single submitter Cardiovascular phenotype
  • p.Leu100= Single submitter Cardiovascular phenotype
  • p.Leu133= Single submitter Cardiovascular phenotype
  • p.Leu144= Single submitter Cardiovascular phenotype
  • p.Leu151= Single submitter Cardiovascular phenotype
  • p.Leu155= Single submitter Cardiovascular phenotype
  • p.Leu159= Single submitter Cardiovascular phenotype
  • p.Leu270= Single submitter Cardiovascular phenotype
  • p.Leu286= Single submitter Cardiovascular phenotype
  • p.Leu46= Single submitter Cardiovascular phenotype
  • p.Leu55= Single submitter Cardiovascular phenotype
  • p.Leu69= Single submitter Cardiovascular phenotype
  • p.Leu70= Single submitter Cardiovascular phenotype
  • p.Leu8= Single submitter Cardiovascular phenotype
  • p.Lys113= Single submitter Cardiovascular phenotype
  • p.Lys93= Single submitter Cardiovascular phenotype
  • p.Phe275= Single submitter Cardiovascular phenotype
  • p.Phe283= Single submitter Cardiovascular phenotype
  • p.Phe51= Single submitter Cardiovascular phenotype
  • p.Pro102= Single submitter Cardiovascular phenotype
  • p.Pro28= Single submitter Cardiovascular phenotype
  • p.Pro285= Single submitter Cardiovascular phenotype
  • p.Ser112= Single submitter Cardiovascular phenotype
  • p.Ser147= Single submitter Cardiovascular phenotype
  • p.Ser308= Single submitter Cardiovascular phenotype
  • p.Thr107= Single submitter Cardiovascular phenotype
  • p.Thr148= Single submitter Cardiovascular phenotype
  • p.Thr243= Single submitter Cardiovascular phenotype
  • p.Thr243Ala Single submitter Cardiovascular phenotype
  • p.Thr26Ala Single submitter Cardiovascular phenotype
  • p.Thr36= Single submitter
  • p.Tyr136= Single submitter Cardiovascular phenotype
  • p.Val179= Single submitter Cardiovascular phenotype
  • p.Val305Leu Single submitter Cardiovascular phenotype
  • c.237-8G>C No assertion criteria APOE-related disorder
  • c.*5C>T No assertion criteria APOE-related disorder
  • p.Arg165= No assertion criteria APOE-related disorder
  • p.Val129= No assertion criteria APOE-related disorder

Uncertain significance 114