KCND3 — 703 ClinVar variants

All ClinVar germline KCND3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 325 flagged for review →

10 Pathogenic · 3 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 33 Conflicting · 24 Benign · 18 Benign/Likely benign · 278 Likely benign · 320 Uncertain significance

Full KCND3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 325

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 agree, ClinVar conflicts 21

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 222

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 222

Predictors split 81

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

All KCND3 variants

Pathogenic 10

Pathogenic/Likely pathogenic 3

  • p.Gly384Ser Multiple submitters hereditary ataxia
  • p.Pro375Ser Multiple submitters spinocerebellar ataxia type 19/22
  • p.Val392Ile Multiple submitters KCND3-associated neurodevelopmental disorder

Likely pathogenic 17

Conflicting classifications of pathogenicity 33

Benign 24

Benign/Likely benign 18

  • c.1106+10C>T Multiple submitters spinocerebellar ataxia type 19/22
  • c.1269+13C>T Multiple submitters spinocerebellar ataxia type 19/22
  • c.1372-6dup Multiple submitters spinocerebellar ataxia type 19/22
  • p.Arg302= Multiple submitters Cardiovascular phenotype
  • p.Asn561= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Asp263= Multiple submitters Cardiovascular phenotype
  • p.Asp39= Multiple submitters Cardiovascular phenotype
  • p.Asp598= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Glu452Lys Multiple submitters Cardiovascular phenotype
  • p.Gly208= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Gly436= Multiple submitters Cardiovascular phenotype
  • p.Ile262= Multiple submitters Cardiovascular phenotype
  • p.Met525Val Multiple submitters Cardiovascular phenotype
  • p.Phe173= Multiple submitters Cardiovascular phenotype
  • p.Pro211= Multiple submitters Cardiovascular phenotype
  • p.Ser319= Multiple submitters Cardiovascular phenotype
  • p.Ser653= Multiple submitters Cardiovascular phenotype
  • p.Thr209= Multiple submitters Cardiovascular phenotype

Likely benign 278

  • c.1270-153G>C Multiple submitters
  • c.1372-34G>A Multiple submitters
  • c.1372-4C>A Multiple submitters spinocerebellar ataxia type 19/22
  • c.1372-4C>T Multiple submitters spinocerebellar ataxia type 19/22
  • c.1519-4G>A Multiple submitters spinocerebellar ataxia type 19/22
  • c.1519-96G>A Multiple submitters
  • c.1766+3G>A Multiple submitters spinocerebellar ataxia type 19/22
  • c.1767-6T>C Multiple submitters spinocerebellar ataxia type 19/22
  • c.*225T>C Multiple submitters
  • p.Ala113= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ala247= Multiple submitters Cardiovascular phenotype
  • p.Ala3= Multiple submitters Cardiovascular phenotype
  • p.Ala342= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ala348= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ala433= Multiple submitters Cardiovascular phenotype
  • p.Ala453= Multiple submitters Cardiovascular phenotype
  • p.Ala6= Multiple submitters Cardiovascular phenotype
  • p.Ala622= Multiple submitters Cardiovascular phenotype
  • p.Ala622Val Multiple submitters spinocerebellar ataxia type 19/22
  • p.Arg107= Multiple submitters Cardiovascular phenotype
  • p.Arg293= Multiple submitters Cardiovascular phenotype
  • p.Asn279= Multiple submitters Cardiovascular phenotype
  • p.Asn45= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Asn451= Multiple submitters Cardiovascular phenotype
  • p.Asn76= Multiple submitters Cardiovascular phenotype
  • p.Asp116= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Asp149= Multiple submitters Cardiovascular phenotype
  • p.Asp512= Multiple submitters Cardiovascular phenotype
  • p.Asp599= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Cys207= Multiple submitters Cardiovascular phenotype
  • p.Cys520= Multiple submitters Cardiovascular phenotype
  • p.Cys547= Multiple submitters Cardiovascular phenotype
  • p.Glu220= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Glu70= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Gly391= Multiple submitters Cardiovascular phenotype
  • p.Gly580= Multiple submitters Cardiovascular phenotype
  • p.His443= Multiple submitters Cardiovascular phenotype
  • p.His478= Multiple submitters Cardiovascular phenotype
  • p.His508= Multiple submitters Cardiovascular phenotype
  • p.Ile272= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ile354= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ile382= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Ile386= Multiple submitters Cardiovascular phenotype
  • p.Ile472= Multiple submitters Cardiovascular phenotype
  • p.Leu245= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Leu29= Multiple submitters Cardiovascular phenotype
  • p.Leu454= Multiple submitters Cardiovascular phenotype
  • p.Leu456= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Lys381= Multiple submitters Cardiovascular phenotype
  • p.Phe192= Multiple submitters Cardiovascular phenotype
  • p.Phe323= Multiple submitters Cardiovascular phenotype
  • p.Phe351= Multiple submitters Cardiovascular phenotype
  • p.Phe383= Multiple submitters Cardiovascular phenotype
  • p.Phe84= Multiple submitters Cardiovascular phenotype
  • p.Pro106= Multiple submitters Cardiovascular phenotype
  • p.Pro161= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Pro176= Multiple submitters Cardiovascular phenotype
  • p.Pro217= Multiple submitters Cardiovascular phenotype
  • p.Pro529= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Pro584= Multiple submitters Cardiovascular phenotype
  • p.Ser164= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Thr100= Multiple submitters Cardiovascular phenotype
  • p.Thr231= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Thr377= Multiple submitters Cardiovascular phenotype
  • p.Thr435= Multiple submitters Cardiovascular phenotype
  • p.Thr53= Multiple submitters Cardiovascular phenotype
  • p.Thr575= Multiple submitters Cardiovascular phenotype
  • p.Tyr108= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Tyr114= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Tyr133= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Tyr187= Multiple submitters spinocerebellar ataxia type 19/22
  • p.Tyr370= Multiple submitters Cardiovascular phenotype
  • p.Val399= Multiple submitters spinocerebellar ataxia type 19/22
  • c.1106+11G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1106+11G>T Single submitter spinocerebellar ataxia type 19/22
  • c.1106+14G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1106+296G>T Single submitter
  • c.1107-12T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1107-21_1107-20del Single submitter spinocerebellar ataxia type 19/22
  • c.1107-7C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1269+14G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1269+17G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1269+18G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1270-18T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1270-20dup Single submitter spinocerebellar ataxia type 19/22
  • c.1270-6T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1371+19T>G Single submitter spinocerebellar ataxia type 19/22
  • c.1371+8C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1372-112dup Single submitter
  • c.1372-13_1372-12insA Single submitter spinocerebellar ataxia type 19/22
  • c.1372-14T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1372-17T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1372-20C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1372-6T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1372-6T>G Single submitter spinocerebellar ataxia type 19/22
  • c.1461+13C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1461+7C>A Single submitter spinocerebellar ataxia type 19/22
  • c.1461+9C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1462-10T>G Single submitter spinocerebellar ataxia type 19/22
  • c.1462-13T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1462-16G>T Single submitter spinocerebellar ataxia type 19/22
  • c.1462-4G>A Single submitter spinocerebellar ataxia type 19/22
  • c.1462-4G>C Single submitter spinocerebellar ataxia type 19/22
  • c.1518+16A>C Single submitter spinocerebellar ataxia type 19/22
  • c.1518+17A>C Single submitter spinocerebellar ataxia type 19/22
  • c.1518+18T>C Single submitter spinocerebellar ataxia type 19/22
  • c.1519-10C>T Single submitter spinocerebellar ataxia type 19/22
  • c.1519-17_1519-15del Single submitter spinocerebellar ataxia type 19/22
  • c.1519-20_1519-18del Single submitter spinocerebellar ataxia type 19/22
  • c.1519-67A>G Single submitter
  • c.1766+224dup Single submitter
  • c.1767-17A>C Single submitter spinocerebellar ataxia type 19/22
  • c.1767-4C>G Single submitter spinocerebellar ataxia type 19/22
  • c.-27del Single submitter
  • c.-30G>A Single submitter
  • c.-36G>C Single submitter
  • c.-47G>C Single submitter
  • c.-72-119T>C Single submitter
  • c.-72-245C>T Single submitter
  • c.-72-284C>A Single submitter
  • c.-73+753A>G Single submitter
  • c.*257dup Single submitter
  • p.Ala119= Single submitter Cardiovascular phenotype
  • p.Ala12= Single submitter spinocerebellar ataxia type 19/22
  • p.Ala194= Single submitter Cardiovascular phenotype
  • p.Ala232= Single submitter Cardiovascular phenotype
  • p.Ala248= Single submitter Cardiovascular phenotype
  • p.Ala285= Single submitter Cardiovascular phenotype
  • p.Ala30Ser Single submitter spinocerebellar ataxia type 19/22
  • p.Ala32= Single submitter spinocerebellar ataxia type 19/22
  • p.Ala453Val Single submitter spinocerebellar ataxia type 19/22
  • p.Ala564= Single submitter spinocerebellar ataxia type 19/22
  • p.Arg139= Single submitter Cardiovascular phenotype
  • p.Arg221= Single submitter spinocerebellar ataxia type 19/22
  • p.Arg256= Single submitter Cardiovascular phenotype
  • p.Arg429= Single submitter Cardiovascular phenotype
  • p.Arg532= Single submitter Cardiovascular phenotype
  • p.Arg55= Single submitter Cardiovascular phenotype
  • p.Arg590= Single submitter Cardiovascular phenotype
  • p.Arg92= Single submitter Cardiovascular phenotype
  • p.Arg99= Single submitter Cardiovascular phenotype
  • p.Asn143= Single submitter
  • p.Asn151= Single submitter Cardiovascular phenotype
  • p.Asn200= Single submitter spinocerebellar ataxia type 19/22
  • p.Asn639Lys Single submitter spinocerebellar ataxia type 19/22
  • p.Asn96= Single submitter Cardiovascular phenotype
  • p.Asp115= Single submitter Cardiovascular phenotype
  • p.Asp152= Single submitter Cardiovascular phenotype
  • p.Asp281= Single submitter Cardiovascular phenotype
  • p.Cys218= Single submitter Cardiovascular phenotype
  • p.Cys482= Single submitter
  • p.Cys93= Single submitter Cardiovascular phenotype
  • p.Gln167= Single submitter Cardiovascular phenotype
  • p.Glu174= Single submitter spinocerebellar ataxia type 19/22
  • p.Glu174Gln Single submitter spinocerebellar ataxia type 19/22
  • p.Glu203= Single submitter spinocerebellar ataxia type 19/22
  • p.Glu320= Single submitter Cardiovascular phenotype
  • p.Glu40= Single submitter Cardiovascular phenotype
  • p.Glu473= Single submitter spinocerebellar ataxia type 19/22
  • p.Glu513= Single submitter Cardiovascular phenotype
  • p.Glu626= Single submitter Cardiovascular phenotype
  • p.Glu77= Single submitter Cardiovascular phenotype
  • p.Glu89= Single submitter Cardiovascular phenotype
  • p.Gly101= Single submitter Cardiovascular phenotype
  • p.Gly129= Single submitter Cardiovascular phenotype
  • p.Gly219= Single submitter Cardiovascular phenotype
  • p.Gly273= Single submitter Cardiovascular phenotype
  • p.Gly306= Single submitter Cardiovascular phenotype
  • p.Gly448= Single submitter Cardiovascular phenotype
  • p.Gly488= Single submitter spinocerebellar ataxia type 19/22
  • p.Gly627= Single submitter Cardiovascular phenotype
  • p.His477= Single submitter spinocerebellar ataxia type 19/22
  • p.Ile123= Single submitter Cardiovascular phenotype
  • p.Ile128= Single submitter Cardiovascular phenotype
  • p.Ile193= Single submitter Cardiovascular phenotype
  • p.Ile333= Single submitter spinocerebellar ataxia type 19/22
  • p.Ile505= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu124= Single submitter Cardiovascular phenotype
  • p.Leu183= Single submitter Cardiovascular phenotype
  • p.Leu216= Single submitter Cardiovascular phenotype
  • p.Leu242= Single submitter Cardiovascular phenotype
  • p.Leu243= Single submitter Cardiovascular phenotype
  • p.Leu274= Single submitter Cardiovascular phenotype
  • p.Leu307= Single submitter Cardiovascular phenotype
  • p.Leu310= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu321= Single submitter Cardiovascular phenotype
  • p.Leu324= Single submitter Cardiovascular phenotype
  • p.Leu389= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu393= Single submitter Cardiovascular phenotype
  • p.Leu442= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu471= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu483= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu497= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu536= Single submitter Cardiovascular phenotype
  • p.Leu562= Single submitter Cardiovascular phenotype
  • p.Leu567= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu586= Single submitter Cardiovascular phenotype
  • p.Leu601= Single submitter spinocerebellar ataxia type 19/22
  • p.Leu9= Single submitter Cardiovascular phenotype
  • p.Lys102= Single submitter Cardiovascular phenotype
  • p.Lys137= Single submitter Cardiovascular phenotype
  • p.Lys140Asn Single submitter Cardiovascular phenotype ⚠
  • p.Lys350= Single submitter spinocerebellar ataxia type 19/22
  • p.Lys467= Single submitter Cardiovascular phenotype
  • p.Lys553= Single submitter Cardiovascular phenotype
  • p.Phe11= Single submitter Cardiovascular phenotype
  • p.Phe227= Single submitter Cardiovascular phenotype
  • p.Phe300= Single submitter Cardiovascular phenotype
  • p.Phe406= Single submitter Cardiovascular phenotype
  • p.Phe74= Single submitter Cardiovascular phenotype
  • p.Phe97= Single submitter Cardiovascular phenotype
  • p.Pro125= Single submitter Cardiovascular phenotype
  • p.Pro206= Single submitter Cardiovascular phenotype
  • p.Pro21= Single submitter Cardiovascular phenotype
  • p.Pro28= Single submitter spinocerebellar ataxia type 19/22
  • p.Pro31= Single submitter Cardiovascular phenotype
  • p.Pro355= Single submitter spinocerebellar ataxia type 19/22
  • p.Pro375= Single submitter Cardiovascular phenotype
  • p.Pro398= Single submitter spinocerebellar ataxia type 19/22
  • p.Pro534= Single submitter Cardiovascular phenotype
  • p.Pro540= Single submitter Cardiovascular phenotype
  • p.Pro558= Single submitter Cardiovascular phenotype
  • p.Pro563= Single submitter Cardiovascular phenotype
  • p.Pro618= Single submitter Cardiovascular phenotype
  • p.Pro62= Single submitter spinocerebellar ataxia type 19/22
  • p.Pro632Leu Single submitter spinocerebellar ataxia type 19/22
  • p.Pro636= Single submitter Cardiovascular phenotype
  • p.Ser112= Single submitter Cardiovascular phenotype
  • p.Ser153= Single submitter Cardiovascular phenotype
  • p.Ser162= Single submitter spinocerebellar ataxia type 19/22
  • p.Ser196= Single submitter Cardiovascular phenotype
  • p.Ser223= Single submitter Cardiovascular phenotype
  • p.Ser260= Single submitter Cardiovascular phenotype
  • p.Ser283= Single submitter Cardiovascular phenotype
  • p.Ser301= Single submitter Cardiovascular phenotype
  • p.Ser304= Single submitter Cardiovascular phenotype
  • p.Ser327= Single submitter Cardiovascular phenotype
  • p.Ser347= Single submitter Cardiovascular phenotype
  • p.Ser357= Single submitter Cardiovascular phenotype
  • p.Ser47= Single submitter Cardiovascular phenotype
  • p.Ser503= Single submitter spinocerebellar ataxia type 19/22
  • p.Ser560= Single submitter Cardiovascular phenotype
  • p.Ser581= Single submitter spinocerebellar ataxia type 19/22
  • p.Thr168= Single submitter Cardiovascular phenotype
  • p.Thr180= Single submitter Cardiovascular phenotype
  • p.Thr204= Single submitter Cardiovascular phenotype
  • p.Thr238= Single submitter Cardiovascular phenotype
  • p.Thr288= Single submitter Cardiovascular phenotype
  • p.Thr313= Single submitter Cardiovascular phenotype
  • p.Thr366= Single submitter spinocerebellar ataxia type 19/22
  • p.Thr367= Single submitter Cardiovascular phenotype
  • p.Thr486= Single submitter spinocerebellar ataxia type 19/22
  • p.Thr502= Single submitter Cardiovascular phenotype
  • p.Thr504= Single submitter Cardiovascular phenotype
  • p.Thr543= Single submitter Cardiovascular phenotype
  • p.Thr565= Single submitter Cardiovascular phenotype
  • p.Thr56Ser Single submitter spinocerebellar ataxia type 19/22
  • p.Thr607= Single submitter spinocerebellar ataxia type 19/22
  • p.Thr611= Single submitter spinocerebellar ataxia type 19/22
  • p.Thr69= Single submitter
  • p.Tyr105= Single submitter Cardiovascular phenotype
  • p.Tyr121= Single submitter Cardiovascular phenotype
  • p.Tyr186= Single submitter Cardiovascular phenotype
  • p.Tyr270= Single submitter Cardiovascular phenotype
  • p.Tyr312= Single submitter spinocerebellar ataxia type 19/22
  • p.Tyr528= Single submitter Cardiovascular phenotype
  • p.Tyr82= Single submitter spinocerebellar ataxia type 19/22
  • p.Tyr98= Single submitter Cardiovascular phenotype
  • p.Val184= Single submitter Cardiovascular phenotype
  • p.Val210= Single submitter Cardiovascular phenotype
  • p.Val239= Single submitter
  • p.Val258= Single submitter Cardiovascular phenotype
  • p.Val338= Single submitter Cardiovascular phenotype
  • p.Val493= Single submitter Cardiovascular phenotype
  • p.Val650= Single submitter spinocerebellar ataxia type 19/22
  • p.Val90= Single submitter Cardiovascular phenotype
  • p.Val94= Single submitter Cardiovascular phenotype
  • p.Glu463= No assertion criteria KCND3-related disorder

Uncertain significance 320

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