Sugi Variant

Sugi Variant/KCNQ2

KCNQ2 — 2285 ClinVar variants

All ClinVar germline KCNQ2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 696 flagged for review →

395 Pathogenic · 93 Pathogenic/Likely pathogenic · 231 Likely pathogenic · 125 Conflicting · 114 Benign · 52 Benign/Likely benign · 589 Likely benign · 686 Uncertain significance

Full KCNQ2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 696

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 7

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

Predictors agree, ClinVar conflicts 73

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

Predicted LoF vs a conflicting call 6

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 347

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 347

Predictors split 263

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 263

All KCNQ2 variants

Pathogenic 395

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

Pathogenic/Likely pathogenic 93

  • c.1149-1G>T Multiple submitters seizures, benign familial neonatal, 1
  • c.1887+1G>T Multiple submitters early-infantile DEE
  • c.297-1G>C Multiple submitters developmental and epileptic encephalopathy, 7
  • c.387+1G>A Multiple submitters early-infantile DEE
  • c.387+2T>C Multiple submitters early-infantile DEE
  • c.927+1G>A Multiple submitters early-infantile DEE
  • p.Ala185Thr Multiple submitters early-infantile DEE ⚠
  • p.Ala193Asp Multiple submitters early-infantile DEE
  • p.Ala193Val Multiple submitters developmental and epileptic encephalopathy, 7 ⚠
  • p.Ala265Ser Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Ala265Thr Multiple submitters early-infantile DEE
  • p.Ala265Val Multiple submitters early-infantile DEE
  • p.Ala294fs Multiple submitters early-infantile DEE
  • p.Ala306Glu Multiple submitters early-infantile DEE
  • p.Ala317Thr Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Ala348Thr Multiple submitters early-infantile DEE ⚠
  • p.Arg144Gln Multiple submitters KCNQ2-Related Disorders
  • p.Arg144Gly Multiple submitters Inborn genetic diseases
  • p.Arg144Trp Multiple submitters early-infantile DEE
  • p.Arg210Cys Multiple submitters early-infantile DEE
  • p.Arg210Pro Multiple submitters early-infantile DEE
  • p.Arg213Gln Multiple submitters early-infantile DEE
  • p.Arg213Leu Multiple submitters seizures, benign familial neonatal, 1
  • p.Arg214Trp Multiple submitters early-infantile DEE
  • p.Arg332Gly Multiple submitters early-infantile DEE
  • p.Arg332Lys Multiple submitters early-infantile DEE
  • p.Arg333Trp Multiple submitters Early-infantile developmental and epileptic encephalopathy
  • p.Arg353Cys Multiple submitters early-infantile DEE ⚠
  • p.Arg547Trp Multiple submitters early-infantile DEE
  • p.Arg560Gln Multiple submitters epilepsy
  • p.Arg560Trp Multiple submitters early-infantile DEE
  • p.Arg581Gln Multiple submitters early-infantile DEE
  • p.Asn258Ser Multiple submitters early-infantile DEE ⚠
  • p.Asp282Asn Multiple submitters early-infantile DEE
  • p.Asp282His Multiple submitters early-infantile DEE
  • p.Gln361Ter Multiple submitters seizures, benign familial neonatal, 1
  • p.Gln375Ter Multiple submitters Inborn genetic diseases
  • p.Gln390Ter Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Gln459Ter Multiple submitters early-infantile DEE
  • p.Gln809Ter Multiple submitters seizures, benign familial neonatal, 1
  • p.Glu231Asp Multiple submitters early-infantile DEE
  • p.Glu749Ter Multiple submitters early-infantile DEE
  • p.Glu778fs Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Gly256Trp Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Gly271Arg Multiple submitters early-infantile DEE
  • p.Gly271Ser Multiple submitters early-infantile DEE
  • p.Gly281Glu Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Gly290Cys Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Gly310Ser Multiple submitters early-infantile DEE
  • p.Gly313Arg Multiple submitters early-infantile DEE
  • p.Gly574Ser Multiple submitters early-infantile DEE
  • p.Gly866fs Multiple submitters developmental and epileptic encephalopathy, 7
  • p.His228Arg Multiple submitters developmental and epileptic encephalopathy, 7
  • p.His260Tyr Multiple submitters early-infantile DEE ⚠
  • p.Ile209Ser Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Ile273Met Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Ile278Thr Multiple submitters early-infantile DEE ⚠
  • p.Leu243Val Multiple submitters early-infantile DEE
  • p.Leu268Phe Multiple submitters early-infantile DEE
  • p.Leu292Pro Multiple submitters early-infantile DEE
  • p.Leu307Pro Multiple submitters early-infantile DEE
  • p.Lys583Asn Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Met1Lys Multiple submitters early-infantile DEE
  • p.Met1Thr Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Met1Val Multiple submitters early-infantile DEE
  • p.Met211Thr Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Met546Ile Multiple submitters Seizure ⚠
  • p.Met565_Val567del Multiple submitters early-infantile DEE
  • p.Met578Val Multiple submitters early-infantile DEE
  • p.Phe240Val Multiple submitters early-infantile DEE
  • p.Phe304Ser Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Phe305del Multiple submitters early-infantile DEE
  • p.Phe305Leu Multiple submitters early-infantile DEE
  • p.Pro285Ser Multiple submitters early-infantile DEE
  • p.Pro308Leu Multiple submitters developmental and epileptic encephalopathy, 7
  • p.Pro335Leu Multiple submitters early-infantile DEE
  • p.Pro411fs Multiple submitters early-infantile DEE
  • p.Pro608fs Multiple submitters Inborn genetic diseases
  • p.Pro652fs Multiple submitters early-infantile DEE
  • p.Ser122Leu Multiple submitters early-infantile DEE
  • p.Ser229Ile Multiple submitters KCNQ2-Related Disorders
  • p.Ser247Leu Multiple submitters early-infantile DEE
  • p.Ser373fs Multiple submitters early-infantile DEE
  • p.Ser507Ter Multiple submitters early-infantile DEE
  • p.Thr217Ile Multiple submitters seizures, benign familial neonatal, 1
  • p.Thr274Met Multiple submitters early-infantile DEE
  • p.Thr276Pro Multiple submitters early-infantile DEE
  • p.Tyr127Cys Multiple submitters early-infantile DEE
  • p.Tyr251Ter Multiple submitters early-infantile DEE
  • p.Tyr363Ter Multiple submitters seizures, benign familial neonatal, 1
  • p.Tyr95Ter Multiple submitters early-infantile DEE
  • p.Val132Met Multiple submitters early-infantile DEE
  • p.Gly279Asp No assertion criteria developmental and epileptic encephalopathy, 7

Likely pathogenic 231

Conflicting classifications of pathogenicity 125

Benign 114

Benign/Likely benign 52

Likely benign 589

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

Uncertain significance 686

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