KCNC1 — 529 ClinVar variants

All ClinVar germline KCNC1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 200 flagged for review →

1 Pathogenic · 4 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 20 Conflicting · 10 Benign · 12 Benign/Likely benign · 201 Likely benign · 269 Uncertain significance

Full KCNC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 200

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 2

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

Predictors agree, ClinVar conflicts 15

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 145

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 37

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

All KCNC1 variants

Pathogenic 1

  • p.Thr400Asn Single submitter progressive myoclonic epilepsy type 7

Pathogenic/Likely pathogenic 4

  • p.Ala421Val Multiple submitters developmental and epileptic encephalopathy
  • p.Arg320His Multiple submitters KCNC1-related disorder
  • p.Thr399Met Multiple submitters Seizure
  • p.Val425Met Multiple submitters progressive myoclonic epilepsy type 7

Likely pathogenic 12

Conflicting classifications of pathogenicity 20

Benign 10

Benign/Likely benign 12

  • c.1504+29C>T Multiple submitters
  • c.570+19A>T Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala239= Multiple submitters Inborn genetic diseases
  • p.Ala429= Multiple submitters Inborn genetic diseases
  • p.Arg228Leu Multiple submitters progressive myoclonic epilepsy type 7
  • p.Arg339= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Gln484Arg Multiple submitters Inborn genetic diseases
  • p.Glu553Asp Multiple submitters Inborn genetic diseases
  • p.Lys304= Multiple submitters Inborn genetic diseases
  • p.Pro528= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ser412= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Tyr543= Multiple submitters progressive myoclonic epilepsy type 7

Likely benign 201

  • c.1505-18C>G Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala243= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala38= Multiple submitters Inborn genetic diseases
  • p.Ala394= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala421= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala423= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ala513= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Arg540= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Asn226Ile Multiple submitters Inborn genetic diseases
  • p.Asn506= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Asp49= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Gln20= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Glu508= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Gly140= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Gly335= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Gly355= Multiple submitters Inborn genetic diseases
  • p.Gly424= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ile274= Multiple submitters Inborn genetic diseases
  • p.Ile389= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Ile435= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Leu26= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Leu324= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Leu415= Multiple submitters Inborn genetic diseases
  • p.Leu426= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Leu490= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Leu68= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Phe258= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Phe359= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Phe439= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Pro461= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Pro489= Multiple submitters Inborn genetic diseases
  • p.Ser277= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Thr108= Multiple submitters Inborn genetic diseases
  • p.Thr231= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Thr535= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Tyr365= Multiple submitters progressive myoclonic epilepsy type 7
  • p.Tyr407= Multiple submitters progressive myoclonic epilepsy type 7
  • c.1504+2376C>T Single submitter
  • c.1504+2422T>C Single submitter
  • c.1504+33C>T Single submitter
  • c.1504+733G>C Single submitter
  • c.1505-11T>C Single submitter progressive myoclonic epilepsy type 7
  • c.1505-14T>C Single submitter progressive myoclonic epilepsy type 7
  • c.1505-17T>C Single submitter progressive myoclonic epilepsy type 7
  • c.1505-20T>C Single submitter progressive myoclonic epilepsy type 7
  • c.1505-2798G>A Single submitter
  • c.1505-8G>A Single submitter progressive myoclonic epilepsy type 7
  • c.1693+10G>A Single submitter progressive myoclonic epilepsy type 7
  • c.1693+36G>A Single submitter
  • c.1693+9A>C Single submitter
  • c.1694-19T>C Single submitter progressive myoclonic epilepsy type 7
  • c.1694-20A>C Single submitter progressive myoclonic epilepsy type 7
  • c.1694-296C>T Single submitter
  • c.570+11A>G Single submitter progressive myoclonic epilepsy type 7
  • c.570+17C>A Single submitter progressive myoclonic epilepsy type 7
  • c.570+93del Single submitter
  • c.571-12T>C Single submitter progressive myoclonic epilepsy type 7
  • c.571-15T>A Single submitter progressive myoclonic epilepsy type 7
  • c.571-172G>A Single submitter
  • c.571-17T>A Single submitter progressive myoclonic epilepsy type 7
  • c.571-9T>A Single submitter progressive myoclonic epilepsy type 7
  • c.*7G>A Single submitter
  • p.Ala115= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala131= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala134= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala136= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala156= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala35= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala353= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala366= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala510= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala512= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala515= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala525= Single submitter progressive myoclonic epilepsy type 7
  • p.Ala80= Single submitter Inborn genetic diseases
  • p.Arg164= Single submitter progressive myoclonic epilepsy type 7
  • p.Arg234= Single submitter progressive myoclonic epilepsy type 7
  • p.Arg311= Single submitter progressive myoclonic epilepsy type 7
  • p.Arg314= Single submitter progressive myoclonic epilepsy type 7
  • p.Arg320= Single submitter progressive myoclonic epilepsy type 7
  • p.Arg59= Single submitter progressive myoclonic epilepsy type 7
  • p.Asn226= Single submitter progressive myoclonic epilepsy type 7
  • p.Asn343= Single submitter progressive myoclonic epilepsy type 7
  • p.Asn516= Single submitter progressive myoclonic epilepsy type 7
  • p.Asp135= Single submitter progressive myoclonic epilepsy type 7
  • p.Asp144= Single submitter progressive myoclonic epilepsy type 7
  • p.Asp282= Single submitter
  • p.Asp305= Single submitter progressive myoclonic epilepsy type 7
  • p.Asp375= Single submitter progressive myoclonic epilepsy type 7
  • p.Asp529= Single submitter progressive myoclonic epilepsy type 7
  • p.Cys267= Single submitter progressive myoclonic epilepsy type 7
  • p.Cys420= Single submitter progressive myoclonic epilepsy type 7
  • p.Cys83= Single submitter progressive myoclonic epilepsy type 7
  • p.Gln3= Single submitter
  • p.Gln372= Single submitter progressive myoclonic epilepsy type 7
  • p.Gln450= Single submitter progressive myoclonic epilepsy type 7
  • p.Glu238= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly145= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly163= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly294= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly297= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly413= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly538= Single submitter progressive myoclonic epilepsy type 7
  • p.Gly544Arg Single submitter progressive myoclonic epilepsy type 7
  • p.Gly95= Single submitter progressive myoclonic epilepsy type 7
  • p.His212= Single submitter progressive myoclonic epilepsy type 7
  • p.His336= Single submitter progressive myoclonic epilepsy type 7
  • p.His383= Single submitter progressive myoclonic epilepsy type 7
  • p.His480= Single submitter progressive myoclonic epilepsy type 7
  • p.His66= Single submitter progressive myoclonic epilepsy type 7
  • p.His77= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile10= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile12= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile204= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile218= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile224= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile248= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile428= Single submitter progressive myoclonic epilepsy type 7
  • p.Ile96= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu119= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu155= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu201= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu295= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu307= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu334= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu34= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu348= Single submitter
  • p.Leu354= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu422= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu514= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu76= Single submitter progressive myoclonic epilepsy type 7
  • p.Leu86= Single submitter progressive myoclonic epilepsy type 7
  • p.Lys153= Single submitter progressive myoclonic epilepsy type 7
  • p.Lys451= Single submitter progressive myoclonic epilepsy type 7
  • p.Lys457Arg Single submitter progressive myoclonic epilepsy type 7
  • p.Lys458= Single submitter progressive myoclonic epilepsy type 7
  • p.Lys568= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe180= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe194= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe198= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe273= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe328= Single submitter progressive myoclonic epilepsy type 7
  • p.Phe391= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro139= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro161= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro183= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro30= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro373= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro40= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro408= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro433= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro464= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro469= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro50= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro578= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro61= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro79= Single submitter progressive myoclonic epilepsy type 7
  • p.Pro85= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser142= Single submitter
  • p.Ser185= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser186= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser296= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser300= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser377= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser379= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser444= Single submitter progressive myoclonic epilepsy type 7
  • p.Ser537= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr17= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr222= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr241= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr25= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr28= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr32= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr337= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr361= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr382= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr399= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr410= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr551= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr585= Single submitter progressive myoclonic epilepsy type 7
  • p.Thr73= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr109= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr22= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr247= Single submitter Inborn genetic diseases
  • p.Tyr290= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr442= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr471= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr48= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr554= Single submitter progressive myoclonic epilepsy type 7
  • p.Tyr87= Single submitter progressive myoclonic epilepsy type 7
  • p.Val227Ala Single submitter
  • p.Val254= Single submitter progressive myoclonic epilepsy type 7
  • p.Val264= Single submitter progressive myoclonic epilepsy type 7
  • p.Val293= Single submitter progressive myoclonic epilepsy type 7
  • p.Val306= Single submitter
  • p.Val312= Single submitter progressive myoclonic epilepsy type 7
  • p.Val316= Single submitter progressive myoclonic epilepsy type 7
  • p.Val475= Single submitter progressive myoclonic epilepsy type 7
  • p.Val572= Single submitter progressive myoclonic epilepsy type 7
  • p.Val82= Single submitter progressive myoclonic epilepsy type 7
  • p.Gln111= No assertion criteria KCNC1-related disorder

Uncertain significance 269