KCNQ3 (O43525) variants and mutations
KCNQ3 (also known as O43525) is a human protein-coding gene encoding a potassium voltage-gated channel subfamily KQT member 3 protein. Together with KCNQ2, its slowly activating current provides much of the neuronal M-current that suppresses repetitive firing. Pathogenic variants can cause self-limited neonatal epilepsy or more severe developmental and epileptic encephalopathy. This analysis covers 1,456 KCNQ3 variants and mutations. Of these, 75% have computational variant effect predictions. Disease context includes Benign familial neonatal seizures, Seizure, and multiple sclerosis. Example KCNQ3 variants include M1T, G2R, and A5S.
Variant analysis overview
- Gene: KCNQ3
- Protein: O43525
- UniProt accession: O43525
- Organism: Homo sapiens
- Variants analyzed: 1456
- Variant scope: all variants
- Completed: 2026-08-18
Variant and mutation evidence
- Variant composition: 1,180 unspecified-consequence records; 1 stop retained variant; 124 synonymous variants; 133 missense variants; 8 frameshift variants; 5 in-frame deletions; 4 stop-gained variants; 1 splice-region variants
- Prediction scores: 1,093 variants have prediction scores (75% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Benign familial neonatal seizures, Seizure, multiple sclerosis, Lambert-Eaton myasthenic syndrome, benign neonatal seizures, myasthenia gravis, epilepsy, hereditary disease, congenital myasthenic syndrome, Congenital myasthenic syndromes, Rolandic epilepsy, Intellectual disability.
Protein structure and variant hotspots
- Protein features: 6 transmembrane segments; 3 binding sites; 2 post-translational modification sites.
- Structural context: 143 variants have structural context.
- PTM context: 5 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable KCNQ3 variants
Examples include M1T, G2R, A5S, A5T, A5V, R6C, R6H, A8E. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1T (p.Met1Thr), rs2130875490, ClinGen CA372293094, ClinVar RCV001368791, MetaLR 0.86, MetaSVM 0.52, Uncertain significance, Benign neonatal seizures
- G2R (p.Gly2Arg), rs2537399064, ClinGen CA372293088, ClinVar RCV003878685, REVEL 0.40, CADD 23.80, Uncertain significance, Benign neonatal seizures
- A5S (p.Ala5Ser), TOPMed rs1554660854, CADD 0.90
- A5T (p.Ala5Thr), rs1554660854, ClinGen CA315658, ClinVar RCV002913130, TOPMed rs1554660854, CADD 1.20, Uncertain significance, Benign neonatal seizures
- A5V (p.Ala5Val), NCI-TCGA TCGA novel, CADD 1.84, Variant assessed as somatic; moderate impact.
- R6C (p.Arg6Cys), 1000Genomes rs535134109, REVEL 0.44, CADD 23.90
- R6H (p.Arg6His), TOPMed rs1382518994, gnomAD rs1382518994, REVEL 0.42, CADD 24.40, Uncertain significance, Benign neonatal seizures; not specified
- A8E (p.Ala8Glu), Ensembl rs1420068758, REVEL 0.43, CADD 23.60
- A8T (p.Ala8Thr), TOPMed rs1163952756, gnomAD rs1163952756, REVEL 0.35, CADD 23.10
- A9V (p.Ala9Val), gnomAD rs1359649725, REVEL 0.39, CADD 23.50
- G10E (p.Gly10Glu), cosmic curated COSV10653, TOPMed rs950610665, gnomAD rs950610665, REVEL 0.53, CADD 23.60
- G10R (p.Gly10Arg), gnomAD rs1822534482, REVEL 0.52, CADD 26.20
- A11E (p.Ala11Glu), Ensembl rs1822534206, REVEL 0.47, CADD 24.10, Uncertain significance
- A11V (p.Ala11Val), rs1822534206, ClinGen CA372293029, ClinVar RCV001042915, NCI-TCGA TCGA novel, REVEL 0.41, CADD 24.10, Uncertain significance, Benign neonatal seizures
- A12S (p.Ala12Ser), rs1352880493, ClinGen CA372293028, ClinVar RCV002570109, gnomAD rs1352880493, REVEL 0.33, CADD 23.40, Uncertain significance, Benign neonatal seizures
- A12V (p.Ala12Val), rs796052672, ClinGen CA315580, ClinVar RCV000187961, ClinVar RCV000806133, REVEL 0.35, CADD 23.80, Conflicting interpretations, not specified; Benign neonatal seizures
- G14C (p.Gly14Cys), TOPMed rs1357758074, REVEL 0.52, CADD 24.70, Uncertain significance
- G14S (p.Gly14Ser), rs1357758074, ClinGen CA372293017, ClinVar RCV002273406, TOPMed rs1357758074, REVEL 0.44, CADD 22.80, Uncertain significance, not provided
- G15D (p.Gly15Asp), rs2537398956, ClinGen CA372293008, ClinVar RCV003749876, NCI-TCGA TCGA novel, REVEL 0.46, CADD 22.60, Uncertain significance, Benign neonatal seizures
- G16C (p.Gly16Cys), TOPMed rs1293079336, gnomAD rs1293079336, REVEL 0.49, CADD 25.20
- D17A (p.Asp17Ala), ExAC rs763797355, gnomAD rs763797355, REVEL 0.38, CADD 22.30
- D17G (p.Asp17Gly), ExAC rs763797355, gnomAD rs763797355, REVEL 0.40, CADD 22.40
- D17N (p.Asp17Asn), rs1355500787, ClinGen CA372292998, ClinVar RCV000647882, gnomAD rs1355500787, REVEL 0.33, CADD 23.30, Uncertain significance, Benign neonatal seizures
- D17Y (p.Asp17Tyr), gnomAD rs1355500787, REVEL 0.37, CADD 23.20, Uncertain significance
- G18R (p.Gly18Arg), rs755333945, ClinGen CA4881032, ClinVar RCV003904493, 1000Genomes rs755333945, REVEL 0.36, CADD 23.30, Uncertain significance, Benign neonatal seizures
- G18W (p.Gly18Trp), rs755333945, ClinGen CA372292991, ClinVar RCV002038787, 1000Genomes rs755333945, REVEL 0.39, CADD 25.90, Uncertain significance, Benign neonatal seizures
- G20C (p.Gly20Cys), rs2130875385, ClinGen CA372292980, ClinVar RCV001906594, Ensembl rs2130875385, REVEL 0.46, CADD 23.70, Uncertain significance, Benign neonatal seizures
- G20D (p.Gly20Asp), rs1822527120, ClinGen CA372292977, ClinVar RCV003253378, Ensembl rs1822527120, REVEL 0.53, CADD 22.60, Uncertain significance, Inborn genetic diseases
- G21R (p.Gly21Arg), rs1822526871, ClinGen CA372292974, ClinVar RCV001039910, Ensembl rs1822526871, REVEL 0.49, CADD 23.90, Uncertain significance, Benign neonatal seizures
- G22D (p.Gly22Asp), TOPMed rs1476334493, REVEL 0.51, CADD 23.10
- G22S (p.Gly22Ser), rs2537398839, ClinGen CA372292967, ClinVar RCV003749941, Uncertain significance, Benign neonatal seizures
- G23D (p.Gly23Asp), Ensembl rs1822526458, REVEL 0.49, CADD 22.20
- G23S (p.Gly23Ser), rs2130875367, ClinGen CA372292962, ClinVar RCV001509349, ClinVar RCV005057464, REVEL 0.38, CADD 22.10, Uncertain significance, not provided; Benign neonatal seizures
- G24R (p.Gly24Arg), rs1822526218, ClinGen CA372292956, ClinVar RCV001372159, ClinVar RCV005040229, REVEL 0.43, CADD 22.80, Uncertain significance, Seizures, benign familial neonatal, 2; Benign neonatal seizures
- G24W (p.Gly24Trp), rs1822526218, ClinGen CA372292954, ClinVar RCV003749253, REVEL 0.50, CADD 25.00, Uncertain significance, Benign neonatal seizures
- A25T (p.Ala25Thr), rs1280461599, ClinGen CA372292950, ClinVar RCV002312424, ClinVar RCV002499304, REVEL 0.41, CADD 22.70, Uncertain significance, Inborn genetic diseases; Benign neonatal seizures; Seizures, benign familial neo
- A26G (p.Ala26Gly), Ensembl rs2130875326
- A26S (p.Ala26Ser), Ensembl rs1023114537, REVEL 0.37, CADD 20.40
- A26V (p.Ala26Val), rs2130875326, ClinGen CA372292942, ClinVar RCV002409898, REVEL 0.34, CADD 22.60, Likely benign, Inborn genetic diseases
- N27K (p.Asn27Lys), TOPMed rs1271630840, gnomAD rs1271630840, REVEL 0.30, CADD 21.70, Likely benign
- N27S (p.Asn27Ser), rs1342457621, ClinGen CA372292935, ClinVar RCV001840916, gnomAD rs1342457621, REVEL 0.27, CADD 22.40, Uncertain significance, not provided
- A29D (p.Ala29Asp), TOPMed rs1227699672, gnomAD rs1227699672, REVEL 0.34, CADD 22.80, Uncertain significance
- A29V (p.Ala29Val), rs1227699672, ClinGen CA372292920, ClinVar RCV002047564, TOPMed rs1227699672, REVEL 0.31, CADD 22.50, Uncertain significance, Benign neonatal seizures
- G30A (p.Gly30Ala), rs1346206352, ClinGen CA372292915, ClinVar RCV002013808, Ensembl rs1346206352, AlphaMissense 0.08, MetaLR 0.80, Uncertain significance, Benign neonatal seizures
- G30E (p.Gly30Glu), Ensembl rs1346206352, REVEL 0.36, AlphaMissense 0.08, Uncertain significance
- G31A (p.Gly31Ala), TOPMed rs1011750724, gnomAD rs1011750724, REVEL 0.33, CADD 23.40, Uncertain significance, not provided
- G31R (p.Gly31Arg), rs1433483426, ClinGen CA372292913, ClinVar RCV001227483, ClinVar RCV002466642, REVEL 0.31, CADD 23.30, Uncertain significance, Benign neonatal seizures
- D32E (p.Asp32Glu), TOPMed rs1416576368, gnomAD rs1416576368, REVEL 0.24, CADD 19.70, Uncertain significance, Inborn genetic diseases
- D32G (p.Asp32Gly), ExAC rs766773660, gnomAD rs766773660, REVEL 0.29, CADD 22.00
- D32H (p.Asp32His), ExAC rs754272127, gnomAD rs754272127, REVEL 0.31, CADD 21.80
- D32Y (p.Asp32Tyr), ExAC rs754272127, gnomAD rs754272127, REVEL 0.33, CADD 22.40
- A33G (p.Ala33Gly), rs761196042, ClinGen CA315660, ClinVar RCV003353439, ExAC rs761196042, REVEL 0.28, CADD 23.30, Uncertain significance, Inborn genetic diseases
- A33V (p.Ala33Val), rs761196042, ClinGen CA4881027, ClinVar RCV001036330, ClinVar RCV003346260, REVEL 0.31, CADD 22.30, Conflicting interpretations, Benign neonatal seizures; Inborn genetic diseases; not specified
- A34E (p.Ala34Glu), rs1412895282, ClinGen CA372292895, ClinVar RCV001092149, gnomAD rs1412895282, REVEL 0.35, CADD 22.80, Uncertain significance, not provided
- A34V (p.Ala34Val), rs1412895282, ClinGen CA372292893, ClinVar RCV002007721, gnomAD rs1412895282, REVEL 0.36, CADD 22.70, Uncertain significance, Benign neonatal seizures
- A36D (p.Ala36Asp), Ensembl rs1822523352, REVEL 0.41, CADD 24.60
- A36P (p.Ala36Pro), ExAC rs767638119, TOPMed rs767638119, gnomAD rs767638119, REVEL 0.44, CADD 23.50, Uncertain significance, Benign neonatal seizures
- A36S (p.Ala36Ser), ExAC rs767638119, TOPMed rs767638119, gnomAD rs767638119, REVEL 0.28, CADD 21.50
- A36V (p.Ala36Val), rs1822523352, ClinGen CA372292882, ClinVar RCV002424281, REVEL 0.35, CADD 23.30, Uncertain significance, Inborn genetic diseases
- G37C (p.Gly37Cys), ExAC rs761996139, TOPMed rs761996139, gnomAD rs761996139, REVEL 0.35, CADD 24.00, Uncertain significance, Benign neonatal seizures; Inborn genetic diseases
- G37S (p.Gly37Ser), rs761996139, ClinGen CA372292881, ClinVar RCV003750277, ExAC rs761996139, REVEL 0.29, CADD 22.60, Uncertain significance, Benign neonatal seizures
- D38E (p.Asp38Glu), rs1477607835, ClinGen CA372292869, ClinVar RCV001349583, gnomAD rs1477607835, REVEL 0.28, CADD 14.80, Uncertain significance, Benign neonatal seizures
- E39* (p.Glu39Ter), rs1448580874, ClinGen CA372292866, ClinVar RCV003586869, CADD 35.00, Pathogenic
- E39D (p.Glu39Asp), TOPMed rs1421966120, gnomAD rs1421966120, REVEL 0.34, CADD 19.60, Uncertain significance, not provided
- E39G (p.Glu39Gly), rs1822522895, ClinGen CA372292864, ClinVar RCV001344130, ClinVar RCV003405576, REVEL 0.36, CADD 22.90, Uncertain significance, Benign neonatal seizures; KCNQ3-related disorder
- E39K (p.Glu39Lys), rs1448580874, TOPMed rs1448580874, gnomAD rs1448580874, REVEL 0.36, CADD 17.60, Uncertain significance
- E39Q (p.Glu39Gln), rs1448580874, ClinGen CA372292867, ClinVar RCV000799577, TOPMed rs1448580874, REVEL 0.32, CADD 20.30, Uncertain significance, Benign neonatal seizures
- E40K (p.Glu40Lys), gnomAD rs1190468863, REVEL 0.40, CADD 21.90
- E40V (p.Glu40Val), Ensembl rs2130875227, REVEL 0.45, CADD 24.40
- R41G (p.Arg41Gly), rs568033682, ClinGen CA4881020, ClinVar RCV003747994, 1000Genomes rs568033682, REVEL 0.43, CADD 23.80, Uncertain significance, Benign neonatal seizures
- R41L (p.Arg41Leu), gnomAD rs867469884, REVEL 0.33, CADD 22.80
- R41Q (p.Arg41Gln), gnomAD rs867469884, REVEL 0.29, CADD 23.10
- K42E (p.Lys42Glu), gnomAD rs1440264080, REVEL 0.31, CADD 24.60
- V43L (p.Val43Leu), NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, REVEL 0.33, CADD 22.10, Variant assessed as somatic; moderate impact.
- V43M (p.Val43Met), rs794726918, ClinGen CA238796, ClinVar RCV000173345, Ensembl rs794726918, REVEL 0.27, CADD 22.80, Uncertain significance, not provided
- G44E (p.Gly44Glu), cosmic curated COSV10748, gnomAD rs1316877906, REVEL 0.54, CADD 23.20
- G44R (p.Gly44Arg), gnomAD rs1198906968, REVEL 0.49, CADD 24.20
- L45P (p.Leu45Pro), ExAC rs769495455, TOPMed rs769495455, gnomAD rs769495455, REVEL 0.53, CADD 24.20, Uncertain significance, Benign neonatal seizures
- L45Q (p.Leu45Gln), ExAC rs769495455, TOPMed rs769495455, gnomAD rs769495455, REVEL 0.51, CADD 24.00, Uncertain significance, not provided
- L45V (p.Leu45Val), ExAC rs775400581, TOPMed rs775400581, gnomAD rs775400581, REVEL 0.34, CADD 19.50
- A46E (p.Ala46Glu), TOPMed rs1452782861, REVEL 0.35, CADD 22.10, Uncertain significance
- A46V (p.Ala46Val), rs1452782861, ClinGen CA372292822, ClinVar RCV002795503, TOPMed rs1452782861, REVEL 0.34, CADD 21.40, Uncertain significance, Benign neonatal seizures
- G48S (p.Gly48Ser), rs1409166665, ClinGen CA372292815, ClinVar RCV001947641, TOPMed rs1409166665, REVEL 0.33, CADD 22.70, Uncertain significance, Benign neonatal seizures
- D49H (p.Asp49His), gnomAD rs886062693, REVEL 0.43, CADD 25.80, Uncertain significance
- D49N (p.Asp49Asn), rs886062693, ClinGen CA10627069, ClinVar RCV000339411, gnomAD rs886062693, REVEL 0.41, CADD 23.00, Uncertain significance, Seizures, benign familial neonatal, 2
- V50E (p.Val50Glu), Ensembl rs1316697709, REVEL 0.47, CADD 16.90, Uncertain significance, Benign neonatal seizures
- V50L (p.Val50Leu), rs1329571058, ClinGen CA372292801, ClinVar RCV002011314, TOPMed rs1329571058, REVEL 0.39, CADD 19.20, Uncertain significance, Benign neonatal seizures
- V50M (p.Val50Met), rs1329571058, ClinGen CA372292802, ClinVar RCV003839665, TOPMed rs1329571058, REVEL 0.34, CADD 21.40, Uncertain significance, Benign neonatal seizures
- E51D (p.Glu51Asp), rs1405186695, ClinGen CA372292790, ClinVar RCV001034787, gnomAD rs1405186695, REVEL 0.32, CADD 18.50, Uncertain significance, Benign neonatal seizures
- E51G (p.Glu51Gly), ExAC rs746592316, gnomAD rs746592316, REVEL 0.38, CADD 23.70
- E51K (p.Glu51Lys), rs1398300403, ClinGen CA372292796, ClinVar RCV003077148, TOPMed rs1398300403, REVEL 0.45, CADD 23.50, Uncertain significance, Benign neonatal seizures
- E51Q (p.Glu51Gln), TOPMed rs1398300403, gnomAD rs1398300403, REVEL 0.42, CADD 24.10, Uncertain significance
- Q52E (p.Gln52Glu), rs1327292650, ClinGen CA372292788, ClinVar RCV000595638, TOPMed rs1327292650, AlphaMissense 0.07, MetaLR 0.81, Uncertain significance, not provided
- Q52H (p.Gln52His), rs2537398473, ClinGen CA372292782, ClinVar RCV002791753, REVEL 0.32, CADD 23.80, Uncertain significance, Benign neonatal seizures
- Q52R (p.Gln52Arg), TOPMed rs1368211262, gnomAD rs1368211262, REVEL 0.40, CADD 22.70
- V53F (p.Val53Phe), gnomAD rs1475773270, REVEL 0.42, CADD 22.70
- A56E (p.Ala56Glu), rs2537398461, ClinGen CA372292759, ClinVar RCV003056410, REVEL 0.64, CADD 19.60, Uncertain significance, Benign neonatal seizures
- A56V (p.Ala56Val), rs2537398461, ClinGen CA372292758, ClinVar RCV003749386, REVEL 0.41, CADD 22.50, Uncertain significance, Benign neonatal seizures
- L57P (p.Leu57Pro), rs886062692, ClinGen CA10624807, ClinVar RCV000334828, gnomAD rs886062692, REVEL 0.50, CADD 24.40, Uncertain significance, Benign neonatal seizures
- L57V (p.Leu57Val), rs1822520331, ClinGen CA372292756, ClinVar RCV003329669, TOPMed rs1822520331, AlphaMissense 0.07, MetaLR 0.91, Uncertain significance, not provided
- G58E (p.Gly58Glu), rs1822520136, ClinGen CA372292748, cosmic curated COSV66483, ClinVar RCV001231303, AlphaMissense 0.17, MetaLR 0.89, Uncertain significance, Benign neonatal seizures
- G58V (p.Gly58Val), rs1822520136, ClinGen CA372292746, ClinVar RCV001560569, Ensembl rs1822520136, REVEL 0.49, AlphaMissense 0.17, Uncertain significance, not provided
- A59D (p.Ala59Asp), NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, REVEL 0.35, CADD 24.50, Variant assessed as somatic; moderate impact.
- A59S (p.Ala59Ser), rs374984158, ClinGen CA4881008, ClinVar RCV002011620, ESP rs374984158, REVEL 0.19, CADD 20.60, Uncertain significance, Benign neonatal seizures
- G60A (p.Gly60Ala), NCI-TCGA Cosmic COSV6646, cosmic curated COSV66468, REVEL 0.49, CADD 22.70, Variant assessed as somatic; moderate impact.
- G60R (p.Gly60Arg), rs1283325203, ClinGen CA372292740, ClinVar RCV001211618, TOPMed rs1283325203, REVEL 0.56, CADD 27.10, Uncertain significance, Benign neonatal seizures
- A61D (p.Ala61Asp), ExAC rs768194589, gnomAD rs768194589, REVEL 0.45, CADD 22.40
- A61N (p.Ala61Asn), rs2537398419, ClinGen CA2580078588, ClinVar RCV003089425, Uncertain significance, Benign neonatal seizures
- A61T (p.Ala61Thr), ExAC rs750884730, TOPMed rs750884730, gnomAD rs750884730, REVEL 0.30, CADD 17.60
- D62E (p.Asp62Glu), rs2537398396, ClinGen CA372292724, ClinVar RCV003587144, REVEL 0.31, CADD 22.50, Uncertain significance, Benign neonatal seizures
- G65A (p.Gly65Ala), rs1822519573, ClinGen CA372292704, ClinVar RCV001200488, Ensembl rs1822519573, AlphaMissense 0.51, MetaLR 0.98, Likely pathogenic, not provided
- G65R (p.Gly65Arg), rs549681789, ClinGen CA4881002, ClinVar RCV001359209, 1000Genomes rs549681789, REVEL 0.76, CADD 26.00, Uncertain significance, Benign neonatal seizures
- G65V (p.Gly65Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G65W (p.Gly65Trp), rs549681789, ClinGen CA372292705, ClinVar RCV001906419, 1000Genomes rs549681789, REVEL 0.75, CADD 32.00, Uncertain significance, Benign neonatal seizures
- T66I (p.Thr66Ile), ExAC rs764387016, gnomAD rs764387016, REVEL 0.43, CADD 24.60
- T66S (p.Thr66Ser), rs2537398377, ClinGen CA372292700, ClinVar RCV004406354, REVEL 0.40, CADD 22.70, Uncertain significance, Benign neonatal seizures
- L69P (p.Leu69Pro), ExAC rs763182139, gnomAD rs763182139, REVEL 0.58, CADD 26.10
- L69Q (p.Leu69Gln), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G71D (p.Gly71Asp), rs2537398343, ClinGen CA372292669, ClinVar RCV003329904, REVEL 0.56, CADD 23.80, Uncertain significance, not provided
- G71S (p.Gly71Ser), rs1822519358, ClinGen CA372292673, ClinVar RCV003749873, gnomAD rs1822519358, REVEL 0.43, CADD 23.40, Uncertain significance, Benign neonatal seizures
- G72C (p.Gly72Cys), ExAC rs759310149, TOPMed rs759310149, gnomAD rs759310149, REVEL 0.36, CADD 23.20, Uncertain significance
- G72S (p.Gly72Ser), rs759310149, ClinGen CA4880997, ClinVar RCV000822042, ClinVar RCV001593018, REVEL 0.37, CADD 19.50, Uncertain significance, Inborn genetic diseases; Benign neonatal seizures; not provided
- G73A (p.Gly73Ala), NCI-TCGA TCGA novel, REVEL 0.43, CADD 22.20, Variant assessed as somatic; moderate impact.
- G73S (p.Gly73Ser), Ensembl rs963533666, REVEL 0.51, CADD 22.90
- R74C (p.Arg74Cys), cosmic curated COSV66464, ExAC rs776548429, gnomAD rs776548429, REVEL 0.52, CADD 26.40
- R74G (p.Arg74Gly), ExAC rs776548429, gnomAD rs776548429, REVEL 0.45, CADD 23.40
- R74H (p.Arg74His), rs1163071564, ClinGen CA372292656, ClinVar RCV001236358, TOPMed rs1163071564, REVEL 0.41, CADD 23.10, Uncertain significance, Benign neonatal seizures
- R74L (p.Arg74Leu), TOPMed rs1163071564, gnomAD rs1163071564, REVEL 0.44, CADD 23.10, Uncertain significance
- R74S (p.Arg74Ser), ExAC rs776548429, gnomAD rs776548429, REVEL 0.46, CADD 23.10
- D75E (p.Asp75Glu), rs138254004, ClinGen CA315582, ClinVar RCV000187962, ClinVar RCV000647892, REVEL 0.29, CADD 12.50, Likely benign, Inborn genetic diseases; Benign neonatal seizures; not specified
- D75N (p.Asp75Asn), NCI-TCGA Cosmic COSV6647, cosmic curated COSV66472, REVEL 0.38, CADD 23.00, Uncertain significance, not provided
- E76D (p.Glu76Asp), Ensembl rs1822518646, REVEL 0.32, CADD 22.20
- E76G (p.Glu76Gly), TOPMed rs1438607992, gnomAD rs1438607992, REVEL 0.36, CADD 25.30
- E76K (p.Glu76Lys), rs747768821, ClinGen CA4880993, ClinVar RCV003041364, ExAC rs747768821, REVEL 0.52, CADD 23.30, Uncertain significance, Benign neonatal seizures
- E76Q (p.Glu76Gln), ExAC rs747768821, TOPMed rs747768821, gnomAD rs747768821, REVEL 0.41, CADD 22.70, Uncertain significance
- E76V (p.Glu76Val), cosmic curated COSV66479, TOPMed rs1438607992, gnomAD rs1438607992, REVEL 0.48, CADD 24.60
- G77R (p.Gly77Arg), TOPMed rs1235793060, gnomAD rs1235793060
- G77W (p.Gly77Trp), TOPMed rs1235793060, gnomAD rs1235793060
- Q78L (p.Gln78Leu), rs2537398279, ClinGen CA372292630, ClinVar RCV003253811, Likely benign, Inborn genetic diseases
- R79Q (p.Arg79Gln), rs778442808, ClinGen CA4880991, ClinVar RCV001961716, ExAC rs778442808, REVEL 0.38, CADD 24.50, Uncertain significance, Benign neonatal seizures
- T81I (p.Thr81Ile), 1000Genomes rs77663285, ExAC rs77663285, TOPMed rs77663285, gnomAD rs77663285, REVEL 0.47, CADD 22.60, Uncertain significance
- T81N (p.Thr81Asn), 1000Genomes rs77663285, ExAC rs77663285, TOPMed rs77663285, gnomAD rs77663285, REVEL 0.30, CADD 21.10, Uncertain significance
- T81P (p.Thr81Pro), Ensembl rs2130874989
- T81S (p.Thr81Ser), rs77663285, ClinGen CA4880990, ClinVar RCV001991924, 1000Genomes rs77663285, REVEL 0.32, CADD 17.60, Uncertain significance, Benign neonatal seizures
- P82L (p.Pro82Leu), gnomAD rs1822518084, REVEL 0.40, CADD 22.90
- Q83P (p.Gln83Pro), rs2537398238, ClinGen CA372292604, ClinVar RCV003586443, REVEL 0.49, CADD 22.90, Uncertain significance, Benign neonatal seizures
- G84A (p.Gly84Ala), ExAC rs781753428, gnomAD rs781753428, REVEL 0.41, CADD 21.80, Uncertain significance
- G84D (p.Gly84Asp), ExAC rs781753428, gnomAD rs781753428, REVEL 0.47, CADD 23.80, Uncertain significance
- G84S (p.Gly84Ser), TOPMed rs1822518036, REVEL 0.47, CADD 22.70
- G84V (p.Gly84Val), rs781753428, ClinGen CA372292595, ClinVar RCV001313926, ExAC rs781753428, REVEL 0.47, CADD 22.80, Uncertain significance, Benign neonatal seizures
- I85L (p.Ile85Leu), rs969479579, ClinGen CA372292594, ClinVar RCV001257258, Ensembl rs969479579, AlphaMissense 0.11, MetaLR 0.78, Uncertain significance, Benign neonatal seizures
- I85T (p.Ile85Thr), gnomAD rs1286727120
- I85V (p.Ile85Val), Ensembl rs969479579, Uncertain significance
- G86A (p.Gly86Ala), NCI-TCGA Cosmic COSV6647, cosmic curated COSV66474, Variant assessed as somatic; moderate impact.
- G86R (p.Gly86Arg), gnomAD rs1239334203, REVEL 0.51, CADD 24.60, Uncertain significance, Benign neonatal seizures
- L87F (p.Leu87Phe), rs752131052, ClinGen CA4880986, ClinVar RCV000793918, ExAC rs752131052, REVEL 0.47, CADD 25.30, Uncertain significance, Benign neonatal seizures
- L87V (p.Leu87Val), ExAC rs752131052, TOPMed rs752131052, gnomAD rs752131052, Uncertain significance
- L88P (p.Leu88Pro), rs1051073307, ClinGen CA372292574, ClinVar RCV002023579, TOPMed rs1051073307, REVEL 0.74, CADD 31.00, Uncertain significance, Benign neonatal seizures
- L88Q (p.Leu88Gln), rs1051073307, ClinGen CA186258324, NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, REVEL 0.71, CADD 29.50, Uncertain significance, Benign neonatal seizures
- P92A (p.Pro92Ala), ExAC rs752955788, gnomAD rs752955788, REVEL 0.68, CADD 24.20
- P92L (p.Pro92Leu), NCI-TCGA Cosmic COSV6646, cosmic curated COSV66467, Variant assessed as somatic; moderate impact.
- P92R (p.Pro92Arg), rs1328966824, ClinGen CA372292550, ClinVar RCV003016678, TOPMed rs1328966824, REVEL 0.71, CADD 29.50, Uncertain significance, Benign neonatal seizures
- L93Q (p.Leu93Gln), TOPMed rs1346150833, gnomAD rs1346150833, REVEL 0.69, CADD 24.20
- S94N (p.Ser94Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S94R (p.Ser94Arg), rs200519334, ClinGen CA4880982, ClinVar RCV001162577, ClinVar RCV002559552, REVEL 0.48, CADD 22.90, Uncertain significance, Benign neonatal seizures; Seizures, benign familial neonatal, 2; Inborn genetic
- R95G (p.Arg95Gly), rs1418381991, NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, gnomAD rs1418381991, REVEL 0.53, CADD 23.40, Variant assessed as somatic; moderate impact.
- R95H (p.Arg95His), NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, REVEL 0.53, CADD 23.90, Variant assessed as somatic; moderate impact.
- V97G (p.Val97Gly), NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, Variant assessed as somatic; moderate impact.
- V97I (p.Val97Ile), rs1377968627, ClinGen CA372292524, ClinVar RCV003748617, ClinVar RCV004775453, REVEL 0.40, CADD 22.20, Uncertain significance, not provided; Benign neonatal seizures
- K98E (p.Lys98Glu), rs1439616512, ClinGen CA372292517, ClinVar RCV003074125, ClinVar RCV004763522, REVEL 0.62, CADD 24.70, Uncertain significance, Benign neonatal seizures; not provided
- K98R (p.Lys98Arg), rs143194379, ClinGen CA4880981, ClinVar RCV000497536, ClinVar RCV002527131, REVEL 0.45, CADD 23.20, Uncertain significance, Seizures, benign familial neonatal, 2; Benign neonatal seizures; not provided
- R99I (p.Arg99Ile), rs1822516917, ClinGen CA372292507, NCI-TCGA Cosmic COSV6646, cosmic curated COSV66467, AlphaMissense 0.81, MetaLR 0.94, Uncertain significance, Benign neonatal seizures
- N101K (p.Asn101Lys), TOPMed rs1433420836, gnomAD rs1433420836, REVEL 0.46, CADD 24.50
- N101S (p.Asn101Ser), rs1822516861, ClinGen CA372292493, ClinVar RCV001988258, TOPMed rs1822516861, REVEL 0.49, CADD 22.90, Uncertain significance, Benign neonatal seizures
- A102P (p.Ala102Pro), TOPMed rs867066299, gnomAD rs867066299, REVEL 0.67, CADD 25.00, Uncertain significance
- A102S (p.Ala102Ser), rs867066299, ClinGen CA186258323, ClinVar RCV003849497, TOPMed rs867066299, REVEL 0.42, CADD 23.60, Uncertain significance, Benign neonatal seizures
- A102T (p.Ala102Thr), TOPMed rs867066299, gnomAD rs867066299, REVEL 0.42, CADD 24.20, Uncertain significance
- K103E (p.Lys103Glu), ExAC rs776460879, gnomAD rs776460879, REVEL 0.54, CADD 23.00
- R105G (p.Arg105Gly), ExAC rs766185814, gnomAD rs766185814, REVEL 0.78, CADD 27.60, Uncertain significance
- R105Q (p.Arg105Gln), NCI-TCGA Cosmic COSV1011, cosmic curated COSV10119, Variant assessed as somatic; moderate impact.
Public KCNQ3 analysis runs
- KCNQ3 analysis run — KCNQ3 (1,456 variants) — completed 2026-08-18