Sugi Variant

Sugi Variant/APOA1

APOA1 — 370 ClinVar variants

All ClinVar germline APOA1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 199 flagged for review →

26 Pathogenic · 2 Pathogenic/Likely pathogenic · 4 Likely pathogenic · 20 Conflicting · 11 Benign · 5 Benign/Likely benign · 103 Likely benign · 199 Uncertain significance

Full APOA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 199

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 1

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

Predictors agree, ClinVar conflicts 10

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

Predictors lean, ClinVar uncertain 101

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

Predictors split 87

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

All APOA1 variants

Pathogenic 26

  • p.Arg197Pro Multiple submitters
  • p.Gln23Ter Multiple submitters hypoalphalipoproteinemia, primary, 2
  • p.Gly50Arg Multiple submitters hypoalphalipoproteinemia, primary, 2
  • c.200+1G>T Single submitter
  • p.Arg34Ter Single submitter
  • p.Leu165Arg Single submitter
  • p.Trp22Ter Single submitter
  • p.Trp74Arg Single submitter amyloidosis, hereditary systemic 3
  • c.43+1G>C No assertion criteria hypoalphalipoproteinemia, primary, 2
  • c.43+1G>T No assertion criteria hereditary spastic paraplegia 50
  • p.Ala199Pro No assertion criteria amyloidosis, hereditary systemic 3
  • p.Arg173Pro No assertion criteria amyloidosis, hereditary systemic 3
  • p.Arg197Cys No assertion criteria APOLIPOPROTEIN A-I (MILANO) ⚠
  • p.Asp44Tyr No assertion criteria amyloidosis, hereditary systemic 3
  • p.Gln108Ter No assertion criteria hypoalphalipoproteinemia, primary, 2
  • p.Gln56Ter No assertion criteria hypoalphalipoproteinemia, primary, 2
  • p.Glu160Ter No assertion criteria hypoalphalipoproteinemia, primary, 2, intermediate
  • p.Leu198Ser No assertion criteria amyloidosis, hereditary systemic 3 ⚠
  • p.Leu202Pro No assertion criteria
  • p.Leu227fs No assertion criteria hypoalphalipoproteinemia, primary, 2
  • p.Leu84_Phe95delinsValThr No assertion criteria amyloidosis, hereditary systemic 3
  • p.Leu84Arg No assertion criteria amyloidosis, hereditary systemic 3
  • p.Lys131Ter No assertion criteria APOLIPOPROTEIN A-I (MARBURG)
  • p.Pro27Arg No assertion criteria APOLIPOPROTEIN A-I (MUNSTER3C) ⚠
  • p.Trp96Arg No assertion criteria amyloidosis, hereditary systemic 3 ⚠
  • p.Val180Glu No assertion criteria hypoalphalipoproteinemia, primary, 2

Pathogenic/Likely pathogenic 2

  • p.His179fs Multiple submitters familial visceral amyloidosis
  • p.Leu99Pro Multiple submitters Cardiovascular phenotype

Likely pathogenic 4

  • p.Ala178fs Single submitter Cardiovascular phenotype
  • p.Asp181Gly Single submitter hypoalphalipoproteinemia, primary, 2 ⚠
  • p.Gln122Ter Single submitter hypoalphalipoproteinemia, primary, 2
  • p.Tyr42Ter Single submitter familial visceral amyloidosis

Conflicting classifications of pathogenicity 20

Benign 11

Benign/Likely benign 5

  • c.200+19G>A Multiple submitters hypoalphalipoproteinemia, primary, 2
  • c.201-9A>G Multiple submitters
  • p.Ala188= Multiple submitters hypoalphalipoproteinemia, primary, 2
  • p.Ala3= Multiple submitters familial visceral amyloidosis
  • p.Val54= Multiple submitters hypoalphalipoproteinemia, primary, 2, intermediate

Likely benign 103

Uncertain significance 199