Sugi Variant

Sugi Variant/SCN3A

SCN3A — 2111 ClinVar variants

All ClinVar germline SCN3A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 1113 flagged for review →

5 Pathogenic · 5 Pathogenic/Likely pathogenic · 31 Likely pathogenic · 78 Conflicting · 68 Benign · 17 Benign/Likely benign · 695 Likely benign · 1212 Uncertain significance

Full SCN3A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 1113

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 40

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

Predicted LoF vs a conflicting call 2

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 770

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 770

Predictors split 300

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 300

All SCN3A variants

Pathogenic 5

  • p.Ile875Thr Expert panel developmental and epileptic encephalopathy
  • p.Phe195fs Expert panel developmental and epileptic encephalopathy
  • p.Gln440Ter Single submitter Inborn genetic diseases
  • p.Leu247Pro Single submitter
  • p.Ser248Pro No assertion criteria epilepsy, familial focal, with variable foci 4 ⚠

Pathogenic/Likely pathogenic 5

  • p.Arg1621Gln Multiple submitters developmental and epileptic encephalopathy, 62
  • p.Glu673Ter Multiple submitters Autosomal dominant SCN3A-related disorders
  • p.Met1765Ile Multiple submitters epilepsy, familial focal, with variable foci 4
  • p.Pro1333Leu Multiple submitters developmental and epileptic encephalopathy, 62
  • p.Thr1486Ile Multiple submitters developmental and epileptic encephalopathy, 62

Likely pathogenic 31

Conflicting classifications of pathogenicity 78

Benign 68

Benign/Likely benign 17

Likely benign 695

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 1212

Showing the top 300 by review status; the full set is in the sitemap.