CACNA1E — 2460 ClinVar variants

All ClinVar germline CACNA1E variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 873 flagged for review →

9 Pathogenic · 6 Pathogenic/Likely pathogenic · 21 Likely pathogenic · 104 Conflicting · 272 Benign · 91 Benign/Likely benign · 1145 Likely benign · 812 Uncertain significance

Full CACNA1E gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 873

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 4

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

Predictors agree, ClinVar conflicts 59

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

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 459

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 459

Predictors split 350

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 350

All CACNA1E variants

Pathogenic 9

  • p.Ala700Thr Single submitter developmental and epileptic encephalopathy
  • p.Arg1219Ter Single submitter Inborn genetic diseases
  • p.Arg572Ter Single submitter Inborn genetic diseases
  • p.Ile1422Phe Single submitter developmental and epileptic encephalopathy
  • p.Ile701Val Single submitter developmental and epileptic encephalopathy, 69 ⚠
  • p.Lys1314Gln Single submitter developmental and epileptic encephalopathy, 69
  • p.Thr1425Asn Single submitter developmental and epileptic encephalopathy
  • p.Ala702Ser No assertion criteria developmental and epileptic encephalopathy, 69
  • p.Gln2220Ter No assertion criteria developmental and epileptic encephalopathy, 69

Pathogenic/Likely pathogenic 6

  • p.Ala702Thr Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Gly348Arg Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Gly352Arg Multiple submitters Inborn genetic diseases
  • p.Ile603Leu Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Leu228Pro Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Phe698Leu Multiple submitters developmental and epileptic encephalopathy, 69

Likely pathogenic 21

Conflicting classifications of pathogenicity 104

Benign 272

Benign/Likely benign 91

  • c.1883+9C>G Multiple submitters developmental and epileptic encephalopathy, 69
  • c.1956+19G>A Multiple submitters developmental and epileptic encephalopathy, 69
  • c.2298-16C>T Multiple submitters developmental and epileptic encephalopathy, 69
  • c.3263-16C>T Multiple submitters developmental and epileptic encephalopathy, 69
  • c.373-14C>T Multiple submitters developmental and epileptic encephalopathy, 69
  • c.4329+14G>A Multiple submitters developmental and epileptic encephalopathy, 69
  • c.4605+12A>C Multiple submitters developmental and epileptic encephalopathy, 69
  • c.4606-7T>C Multiple submitters developmental and epileptic encephalopathy, 69
  • c.4816-3C>T Multiple submitters developmental and epileptic encephalopathy, 69
  • c.4882-6_4882-4del Multiple submitters developmental and epileptic encephalopathy, 69
  • c.6399+3G>A Multiple submitters developmental and epileptic encephalopathy, 69
  • p.835GLAL[1] Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ala10Ser Multiple submitters Inborn genetic diseases
  • p.Ala1516= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ala2109Pro Multiple submitters Inborn genetic diseases
  • p.Ala2179= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ala2179Val Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ala2241Thr Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ala396Thr Multiple submitters Inborn genetic diseases
  • p.Ala450Ser Multiple submitters Inborn genetic diseases
  • p.Ala645= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg1121Cys Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Arg1121His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg1901Cys Multiple submitters Inborn genetic diseases
  • p.Arg1932Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg1963Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg1997Met Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg2019His Multiple submitters Inborn genetic diseases
  • p.Arg2116His Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Arg2120Lys Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Arg2157Gln Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Arg2177Gln Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg2284Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg2286Gln Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg444Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg831Thr Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg849His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg863Gln Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Arg919Gln Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Arg938Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Asn1241= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Asn2204Asp Multiple submitters Inborn genetic diseases
  • p.Asp1635= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Asp959Ala Multiple submitters Inborn genetic diseases
  • p.Gln1048Arg Multiple submitters Inborn genetic diseases
  • p.Gln373= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Gln41Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Glu1181= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Glu1328Asp Multiple submitters Inborn genetic diseases
  • p.Glu2190Lys Multiple submitters Inborn genetic diseases ⚠
  • p.Glu2209Lys Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Gly177Glu Multiple submitters Inborn genetic diseases
  • p.Gly2281Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Gly998Ser Multiple submitters developmental and epileptic encephalopathy, 69
  • p.His754Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.His889Asp Multiple submitters Inborn genetic diseases
  • p.His923Arg Multiple submitters Inborn genetic diseases
  • p.Ile1515= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Leu766= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Met2278Val Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Met523Ile Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Phe1279= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Phe1578= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Phe341= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Pro1904Leu Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Pro1904Thr Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Pro1940= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Pro2293Leu Multiple submitters Inborn genetic diseases
  • p.Pro31Leu Multiple submitters Inborn genetic diseases
  • p.Pro803Leu Multiple submitters Inborn genetic diseases
  • p.Pro824Ser Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Pro894Leu Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser1049= Multiple submitters
  • p.Ser1069= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser1180Leu Multiple submitters Inborn genetic diseases
  • p.Ser19= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser351= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser405= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser436= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Ser776= Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Thr1022Met Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Thr2208Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Thr2307Met Multiple submitters Inborn genetic diseases
  • p.Tyr2172Cys Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Val1019Met Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Val1077Met Multiple submitters developmental and epileptic encephalopathy, 69 ⚠
  • p.Val1701Met Multiple submitters Inborn genetic diseases ⚠
  • p.Val1747Ile Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Val1883Met Multiple submitters Inborn genetic diseases
  • p.Val926Ile Multiple submitters developmental and epileptic encephalopathy, 69
  • p.Val989= Multiple submitters developmental and epileptic encephalopathy, 69

Likely benign 1145

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

Uncertain significance 812

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