PAX6 — 917 ClinVar variants

All ClinVar germline PAX6 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

272 Pathogenic · 22 Pathogenic/Likely pathogenic · 97 Likely pathogenic · 49 Conflicting · 46 Benign · 16 Benign/Likely benign · 160 Likely benign · 255 Uncertain significance

Full PAX6 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 166

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.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 124

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

Predictors split 25

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

All PAX6 variants

Pathogenic 272

Pathogenic/Likely pathogenic 22

Likely pathogenic 97

Conflicting classifications of pathogenicity 49

Benign 46

Benign/Likely benign 16

  • c.-129+9G>A Multiple submitters autosomal dominant keratitis
  • c.*2416G>T Multiple submitters foveal hypoplasia 1
  • c.*2901T>C Multiple submitters carboxymethyl-dextran-A2-gadolinium-DOTA
  • c.*2985G>A Multiple submitters WAGR syndrome
  • c.*3885G>T Multiple submitters WAGR syndrome
  • c.*5108A>G Multiple submitters WAGR syndrome
  • c.*842G>A Multiple submitters foveal hypoplasia 1
  • p.Arg44= Multiple submitters aniridia 1
  • p.Glu123= Multiple submitters Anophthalmia-microphthalmia syndrome
  • p.Ter437= Multiple submitters PAX6-related ocular dysgenesis
  • c.*1436G>A Single submitter Anophthalmia-microphthalmia syndrome
  • c.*1478C>T Single submitter carboxymethyl-dextran-A2-gadolinium-DOTA
  • c.*2697T>A Single submitter carboxymethyl-dextran-A2-gadolinium-DOTA
  • c.*4370C>G Single submitter WAGR syndrome
  • c.*4599T>G Single submitter WAGR syndrome
  • p.Gln436Lys No assertion criteria

Likely benign 160

Uncertain significance 255