Sugi Variant

Sugi Variant/KCNQ3

KCNQ3 — 1453 ClinVar variants

All ClinVar germline KCNQ3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 581 flagged for review →

23 Pathogenic · 7 Pathogenic/Likely pathogenic · 26 Likely pathogenic · 81 Conflicting · 152 Benign · 40 Benign/Likely benign · 398 Likely benign · 726 Uncertain significance

Full KCNQ3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 581

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 35

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

Predicted LoF vs a conflicting call 9

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 395

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 395

Predictors split 141

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

All KCNQ3 variants

Pathogenic 23

  • p.Ala475fs Single submitter benign neonatal seizures
  • p.Arg230Ser Single submitter intellectual disability
  • p.Arg330Leu Single submitter benign neonatal seizures
  • p.Asn100fs Single submitter benign neonatal seizures
  • p.Asn27fs Single submitter benign neonatal seizures
  • p.Gln360Ter Single submitter benign neonatal seizures
  • p.Gln422Ter Single submitter benign neonatal seizures
  • p.Gln526Ter Single submitter benign neonatal seizures
  • p.Glu298fs Single submitter benign neonatal seizures
  • p.Glu39Ter Single submitter benign neonatal seizures
  • p.Gly20_Gly21insTer Single submitter benign neonatal seizures
  • p.Gly268Arg Single submitter benign neonatal seizures
  • p.Gly320Arg Single submitter benign neonatal seizures
  • p.Gly354Arg Single submitter
  • p.Gly575fs Single submitter benign neonatal seizures
  • p.Ile350fs Single submitter benign neonatal seizures
  • p.Met237Lys Single submitter benign neonatal seizures
  • p.Ser407fs Single submitter benign neonatal seizures
  • p.Tyr563fs Single submitter benign neonatal seizures
  • p.Ala381Val No assertion criteria self-limited epilepsy with centrotemporal spikes
  • p.Glu170Gly No assertion criteria Seizure
  • p.Gly310Val No assertion criteria seizures, benign familial neonatal, 2
  • p.Trp309Arg No assertion criteria seizures, benign familial neonatal, 2

Pathogenic/Likely pathogenic 7

  • p.Ala306Val Multiple submitters benign neonatal seizures
  • p.Arg230Cys Multiple submitters KCNQ3-related disorder
  • p.Arg230His Multiple submitters KCNQ3-related disorder
  • p.Arg330Cys Multiple submitters KCNQ3-related disorder
  • p.Arg330His Multiple submitters KCNQ3-related disorder
  • p.Arg364His Multiple submitters benign neonatal seizures
  • p.Ile317Thr Multiple submitters seizures, benign familial neonatal, 2

Likely pathogenic 26

Conflicting classifications of pathogenicity 81

Benign 152

Benign/Likely benign 40

  • c.1236-16C>T Multiple submitters benign neonatal seizures
  • c.1568+12A>G Multiple submitters benign neonatal seizures
  • c.1568+14G>A Multiple submitters seizures, benign familial neonatal, 2
  • c.1568+15G>A Multiple submitters seizures, benign familial neonatal, 2
  • c.1701-17C>T Multiple submitters benign neonatal seizures
  • c.1885-5dup Multiple submitters benign neonatal seizures
  • c.778-17A>C Multiple submitters benign neonatal seizures
  • c.-65C>T Multiple submitters seizures, benign familial neonatal, 2
  • c.-7G>C Multiple submitters
  • c.-85C>T Multiple submitters seizures, benign familial neonatal, 2
  • c.*1697C>G Multiple submitters seizures, benign familial neonatal, 2
  • c.*2166A>G Multiple submitters seizures, benign familial neonatal, 2
  • c.*2847T>C Multiple submitters seizures, benign familial neonatal, 2
  • c.*3823G>A Multiple submitters seizures, benign familial neonatal, 2
  • c.*4258T>C Multiple submitters seizures, benign familial neonatal, 2
  • c.*4817G>A Multiple submitters seizures, benign familial neonatal, 2
  • c.*5255T>C Multiple submitters seizures, benign familial neonatal, 2
  • c.*5965T>C Multiple submitters seizures, benign familial neonatal, 2
  • c.*7413G>C Multiple submitters seizures, benign familial neonatal, 2
  • c.*7464C>A Multiple submitters seizures, benign familial neonatal, 2
  • p.Ala517= Multiple submitters Inborn genetic diseases
  • p.Arg649= Multiple submitters benign neonatal seizures
  • p.Arg80= Multiple submitters benign neonatal seizures
  • p.Asp542= Multiple submitters benign neonatal seizures
  • p.Asp569= Multiple submitters benign neonatal seizures
  • p.Asp755Asn Multiple submitters Inborn genetic diseases
  • p.Gln653Arg Multiple submitters seizures, benign familial neonatal, 2
  • p.Gly691Ser Multiple submitters benign neonatal seizures
  • p.Gly723Glu Multiple submitters Inborn genetic diseases
  • p.Leu278= Multiple submitters Inborn genetic diseases
  • p.Leu639= Multiple submitters Inborn genetic diseases
  • p.Leu754= Multiple submitters benign neonatal seizures
  • p.Phe699= Multiple submitters benign neonatal seizures
  • p.Pro574Ser Multiple submitters benign neonatal seizures ⚠
  • p.Pro693= Multiple submitters benign neonatal seizures
  • p.Pro769His Multiple submitters benign neonatal seizures
  • p.Ser353= Multiple submitters Inborn genetic diseases
  • p.Thr316= Multiple submitters Inborn genetic diseases
  • p.Thr783= Multiple submitters benign neonatal seizures
  • p.Tyr710His Multiple submitters benign neonatal seizures

Likely benign 398

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

Uncertain significance 726

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