Sugi Variant

Sugi Variant/KCNA3

KCNA3 — 117 ClinVar variants

All ClinVar germline KCNA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 91 flagged for review →

16 Likely pathogenic · 3 Benign · 1 Benign/Likely benign · 8 Likely benign · 89 Uncertain significance

Full KCNA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 91

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 3

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

Predictors lean, ClinVar uncertain 75

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

Predictors split 13

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

All KCNA3 variants

Likely pathogenic 16

  • p.Pro477His Multiple submitters KCNA3-associated disorder
  • p.Thr443Ile Multiple submitters KCNA3-associated developmental and epileptic encephalopathy
  • p.Ala357Val Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Ala361Thr Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Gly456Arg Single submitter KCNA3-associated disorder
  • p.Gly468Arg Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Gly468Phe Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Gly468Val Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Ile431Asn Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Ile455Val Single submitter KCNA3-associated developmental and epileptic encephalopathy ⚠
  • p.Pro11Arg Single submitter KCNA3-associated developmental and epileptic encephalopathy ⚠
  • p.Pro475Arg Single submitter
  • p.Ser525Asn Single submitter KCNA3-associated developmental and epileptic encephalopathy ⚠
  • p.Tyr487Cys Single submitter Inborn genetic diseases
  • p.Val460Met Single submitter KCNA3-associated developmental and epileptic encephalopathy
  • p.Val478Met Single submitter KCNA3-associated developmental and epileptic encephalopathy

Benign 3

Benign/Likely benign 1

Likely benign 8

Uncertain significance 89