SCN1A — 2683 ClinVar variants

All ClinVar germline SCN1A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 826 flagged for review →

763 Pathogenic · 123 Pathogenic/Likely pathogenic · 325 Likely pathogenic · 184 Conflicting · 78 Benign · 26 Benign/Likely benign · 400 Likely benign · 784 Uncertain significance

Full SCN1A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 826

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 20

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

Predictors agree, ClinVar conflicts 101

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

Predictors lean, ClinVar uncertain 466

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 466

Predictors split 239

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 239

All SCN1A variants

Pathogenic 763

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

Pathogenic/Likely pathogenic 123

  • c.1028+1del Multiple submitters Dravet syndrome
  • c.1171-1G>A Multiple submitters early-infantile DEE
  • c.1377+1G>A Multiple submitters Dravet syndrome
  • c.1662+1G>T Multiple submitters SCN1A-related disorder
  • c.1662+3A>G Multiple submitters early-infantile DEE
  • c.1663-2A>G Multiple submitters Inborn genetic diseases
  • c.2589+2dup Multiple submitters Dravet syndrome
  • c.264+1G>A Multiple submitters early-infantile DEE
  • c.264+4_264+7del Multiple submitters early-infantile DEE
  • c.264+5G>A Multiple submitters early-infantile DEE
  • c.2946+5G>A Multiple submitters early-infantile DEE
  • c.4581+5G>C Multiple submitters early-infantile DEE
  • c.4582-2A>G Multiple submitters SCN1A-related disorder
  • c.473+5G>A Multiple submitters early-infantile DEE
  • c.473+5G>C Multiple submitters early-infantile DEE
  • c.602+1del Multiple submitters Dravet syndrome
  • c.602+2dup Multiple submitters early-infantile DEE
  • c.965-1G>A Multiple submitters early-infantile DEE
  • p.Ala121Pro Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Ala1662Val Multiple submitters Inborn genetic diseases
  • p.Ala175Thr Multiple submitters early-infantile DEE
  • p.Ala239Val Multiple submitters SCN1A-related disorder
  • p.Ala342Ser Multiple submitters Dravet syndrome ⚠
  • p.Ala395Asp Multiple submitters early-infantile DEE
  • p.Ala425fs Multiple submitters Autosomal dominant epilepsy
  • p.Ala889Thr Multiple submitters early-infantile DEE
  • p.Ala989Val Multiple submitters early-infantile DEE
  • p.Arg101Trp Multiple submitters SCN1A-related disorder
  • p.Arg118Ser Multiple submitters Dravet syndrome
  • p.Arg1861Trp Multiple submitters Seizure
  • p.Arg222Ter Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Arg377Gln Multiple submitters early-infantile DEE
  • p.Arg377Leu Multiple submitters SCN1A-related disorder
  • p.Arg393Cys Multiple submitters early-infantile DEE
  • p.Arg393His Multiple submitters SCN1A-related disorder
  • p.Arg862Leu Multiple submitters early-infantile DEE
  • p.Arg862Ter Multiple submitters early-infantile DEE
  • p.Arg865Gln Multiple submitters early-infantile DEE
  • p.Arg931Cys Multiple submitters early-infantile DEE
  • p.Arg931Leu Multiple submitters Dravet syndrome
  • p.Arg931Pro Multiple submitters early-infantile DEE
  • p.Arg931Ser Multiple submitters Dravet syndrome
  • p.Arg946His Multiple submitters SCN1A-related disorder
  • p.Arg946Pro Multiple submitters Dravet syndrome
  • p.Asn1672His Multiple submitters SCN1A-related disorder
  • p.Asp1608Tyr Multiple submitters early-infantile DEE
  • p.Asp194Asn Multiple submitters early-infantile DEE
  • p.Asp194Tyr Multiple submitters early-infantile DEE
  • p.Asp366His Multiple submitters early-infantile DEE
  • p.Cys1588Arg Multiple submitters early-infantile DEE
  • p.Cys1716Arg Multiple submitters early-infantile DEE
  • p.Cys257Arg Multiple submitters Dravet syndrome
  • p.Cys277Tyr Multiple submitters Dravet syndrome
  • p.Cys345Phe Multiple submitters early-infantile DEE
  • p.Cys737fs Multiple submitters SCN1A-related disorder
  • p.Cys927Arg Multiple submitters early-infantile DEE
  • p.Cys959Arg Multiple submitters early-infantile DEE
  • p.Cys968Tyr Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Gln1923His Multiple submitters early-infantile DEE
  • p.Gln910Arg Multiple submitters early-infantile DEE
  • p.Gln928Ter Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Glu435fs Multiple submitters Dravet syndrome
  • p.Gly1275Asp Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Gly1365Asp Multiple submitters early-infantile DEE
  • p.Gly1754Glu Multiple submitters early-infantile DEE
  • p.Gly271Ser Multiple submitters Dravet syndrome
  • p.Gly271Val Multiple submitters early-infantile DEE
  • p.Gly329Ala Multiple submitters early-infantile DEE
  • p.Gly329Cys Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Gly329Val Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Gly343Arg Multiple submitters SCN1A-related disorder ⚠
  • p.Gly343Asp Multiple submitters Inborn genetic diseases
  • p.Gly682Ter Multiple submitters SCN1A-related disorder
  • p.His933Tyr Multiple submitters Inborn genetic diseases
  • p.His939Tyr Multiple submitters Dravet syndrome
  • p.Ile138Ser Multiple submitters SCN1A-related disorder
  • p.Ile173Asn Multiple submitters early-infantile DEE
  • p.Ile1922Thr Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Ile227Thr Multiple submitters migraine, familial hemiplegic, 3
  • p.Ile252Asn Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Ile415Lys Multiple submitters early-infantile DEE
  • p.Ile91Thr Multiple submitters SCN1A-related disorder
  • p.Leu117Pro Multiple submitters early-infantile DEE
  • p.Leu1621Pro Multiple submitters early-infantile DEE
  • p.Leu180Ter Multiple submitters early-infantile DEE
  • p.Leu221Pro Multiple submitters Dravet syndrome
  • p.Leu373Ser Multiple submitters early-infantile DEE
  • p.Leu378fs Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Leu390Pro Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Leu77Pro Multiple submitters early-infantile DEE
  • p.Leu991Phe Multiple submitters Dravet syndrome
  • p.Lys1492= Multiple submitters early-infantile DEE
  • p.Met785fs Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Met934Arg Multiple submitters early-infantile DEE
  • p.Met956Thr Multiple submitters early-infantile DEE
  • p.Met976Thr Multiple submitters early-infantile DEE
  • p.Phe1765Ser Multiple submitters Dravet syndrome
  • p.Phe403Leu Multiple submitters early-infantile DEE
  • p.Phe784fs Multiple submitters early-infantile DEE
  • p.Phe90Ser Multiple submitters early-infantile DEE
  • p.Pro113Leu Multiple submitters SCN1A-related disorder
  • p.Pro113Ser Multiple submitters epilepsy
  • p.Pro189fs Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Ser1328Pro Multiple submitters early-infantile DEE
  • p.Ser259Arg Multiple submitters Dravet syndrome
  • p.Ser872Tyr Multiple submitters Dravet syndrome ⚠
  • p.Ser940Phe Multiple submitters early-infantile DEE
  • p.Thr105Ile Multiple submitters
  • p.Thr160Asn Multiple submitters early-infantile DEE
  • p.Thr162Ile Multiple submitters early-infantile DEE ⚠
  • p.Thr363Pro Multiple submitters early-infantile DEE
  • p.Thr875Met Multiple submitters early-infantile DEE
  • p.Tyr165His Multiple submitters developmental and epileptic encephalopathy 6B
  • p.Tyr325del Multiple submitters obesity disorder
  • p.Tyr426Cys Multiple submitters early-infantile DEE
  • p.Tyr790Phe Multiple submitters early-infantile DEE ⚠
  • p.Tyr84Cys Multiple submitters generalized epilepsy with febrile seizures plus, type 2
  • p.Val1534Asp Multiple submitters Dravet syndrome
  • p.Val421Met Multiple submitters Dravet syndrome
  • p.Val422Met Multiple submitters early-infantile DEE
  • p.Val887Glu Multiple submitters Autosomal dominant SCN1A-related disorders
  • p.Val896Ile Multiple submitters early-infantile DEE
  • p.Val983Ile Multiple submitters early-infantile DEE

Likely pathogenic 325

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

Conflicting classifications of pathogenicity 184

Benign 78

Benign/Likely benign 26

Likely benign 400

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

Uncertain significance 784

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