KCNMA1 (Q12791) variants and mutations
KCNMA1 (also known as Q12791) is a human protein-coding gene encoding a calcium-activated potassium channel subunit alpha-1 protein. Its large-conductance potassium current couples membrane voltage and intracellular calcium to rapid repolarization in neurons, smooth muscle, and other excitable cells. Gain- and loss-of-function variants can cause paroxysmal dyskinesia, epilepsy, developmental impairment, and movement disorders. This analysis covers 1,392 KCNMA1 variants and mutations. Of these, 68% have computational variant effect predictions. Disease context includes Generalized epilepsy - paroxysmal dyskinesia, generalized epilepsy-paroxysmal dyskinesia syndrome, and Liang-Wang syndrome. Example KCNMA1 variants include M1L, M1V, and A2P.
Variant analysis overview
- Gene: KCNMA1
- Protein: Q12791
- UniProt accession: Q12791
- Organism: Homo sapiens
- Variants analyzed: 1392
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 1,173 unspecified-consequence records; 4 stop lost; 1 stop retained variant; 123 missense variants; 69 synonymous variants; 2 in-frame deletions; 10 stop-gained variants; 7 frameshift variants; 2 splice-region variants; 1 in-frame insertions
- Prediction scores: 950 variants have prediction scores (68% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Generalized epilepsy - paroxysmal dyskinesia, generalized epilepsy-paroxysmal dyskinesia syndrome, Liang-Wang syndrome, cerebellar atrophy, developmental delay, and seizures, idiopathic generalized epilepsy, hereditary disease, myopia, osteoarthritis, hip, refractive error, injury, diabetes mellitus, muscular disease.
Protein structure and variant hotspots
- Protein features: 7 transmembrane segments; 2 domains; 7 binding sites; 9 post-translational modification sites.
- Structural context: 345 variants have structural context.
- PTM context: 13 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable KCNMA1 variants
Examples include M1L, M1V, A2P, A2Q, A2T, G4S, G5D, G6S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1L (p.Met1Leu), rs1232656132, ClinGen CA377412971, ClinVar RCV003318990, MetaLR 0.31, MetaSVM -0.80, Uncertain significance, not provided
- M1V (p.Met1Val), rs1232656132, ClinGen CA377412970, ClinVar RCV003076624, MetaLR 0.31, MetaSVM -0.80, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A2P (p.Ala2Pro), rs1344908173, ClinGen CA377412962, ClinVar RCV004552571, AlphaMissense 0.30, MetaLR 0.29, Uncertain significance, KCNMA1-related disorder
- A2Q (p.Ala2Gln), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- A2T (p.Ala2Thr), rs1344908173, ClinGen CA377412960, ClinVar RCV001301840, ClinVar RCV005414592, AlphaMissense 0.30, MetaLR 0.29, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- G4S (p.Gly4Ser), gnomAD rs1299022120, CADD 26.60, PolyPhen-2 0.85
- G5D (p.Gly5Asp), ExAC rs773490198, gnomAD rs773490198, CADD 22.20, PolyPhen-2 0.01
- G6S (p.Gly6Ser), rs914048941, ClinGen CA210159570, ClinVar RCV000639889, ClinVar RCV001252027, CADD 23.20, PolyPhen-2 0.00, Uncertain significance, Inborn genetic diseases; not provided; Generalized epilepsy-paroxysmal dyskinesi
- G7D (p.Gly7Asp), gnomAD rs1286114059, CADD 23.30, PolyPhen-2 0.01
- G8S (p.Gly8Ser), TOPMed rs988282616, gnomAD rs988282616, CADD 24.10, PolyPhen-2 0.86
- G9D (p.Gly9Asp), gnomAD rs1326570648, CADD 23.20, PolyPhen-2 0.02
- G10C (p.Gly10Cys), rs776683537, ClinGen CA377412914, ClinVar RCV002840281, CADD 20.60, PolyPhen-2 0.15, Uncertain significance, Inborn genetic diseases
- G10S (p.Gly10Ser), rs776683537, ClinGen CA5568827, cosmic curated COSV54239, ClinVar RCV002918026, CADD 19.10, PolyPhen-2 0.00, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- S11R (p.Ser11Arg), TOPMed rs2093902959, CADD 22.10, PolyPhen-2 0.00
- S11G (p.Ser11Gly), rs886047270, ClinGen CA5568824, cosmic curated COSV54238, ClinVar RCV000370095, CADD 19.30, PolyPhen-2 0.00, Uncertain significance, KCNMA1-related disorder; Inborn genetic diseases; Generalized epilepsy-paroxysma
- S11N (p.Ser11Asn), TOPMed rs2093903843, CADD 15.00, PolyPhen-2 0.00
- S12G (p.Ser12Gly), rs77602559, ClinGen CA200416, ClinVar RCV000173273, ClinVar RCV000298996, CADD 21.00, PolyPhen-2 0.00, Benign/Likely benign, not specified; not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- S12N (p.Ser12Asn), 1000Genomes rs553253349, CADD 22.50, PolyPhen-2 0.00
- G13D (p.Gly13Asp), gnomAD rs1182008461
- G13S (p.Gly13Ser), rs1568036609, ClinGen CA377412896, cosmic curated COSV54228, ClinVar RCV001107254, CADD 22.80, PolyPhen-2 0.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G14S (p.Gly14Ser), TOPMed rs997594261, CADD 23.50, PolyPhen-2 0.00
- G15D (p.Gly15Asp), rs2093899892, ClinGen CA377412883, ClinVar RCV003060733, Ensembl rs2093899892, AlphaMissense 0.31, MetaLR 0.33, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G16S (p.Gly16Ser), rs1568035847, ClinGen CA377412880, ClinVar RCV002938214, ClinVar RCV004738633, CADD 23.60, PolyPhen-2 0.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G17R (p.Gly17Arg), rs886047269, ClinGen CA10632329, ClinVar RCV000357305, Ensembl rs886047269, AlphaMissense 0.44, MetaLR 0.05, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G17S (p.Gly17Ser), Ensembl rs886047269, CADD 0.17, Uncertain significance
- G17D (p.Gly17Asp), gnomAD rs1180407859, CADD 1.18
- G18D (p.Gly18Asp), gnomAD rs1275894827, CADD 23.50, PolyPhen-2 0.02
- G19V (p.Gly19Val), Ensembl rs199979410
- G19R (p.Gly19Arg), rs2154572188, ClinGen CA377412863, ClinVar RCV001363966, Ensembl rs2154572188, CADD 24.10, PolyPhen-2 0.01, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G20D (p.Gly20Asp), rs888320237, ClinGen CA210159560, ClinVar RCV001295223, ClinVar RCV003456487, CADD 23.60, PolyPhen-2 0.01, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- G20S (p.Gly20Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S21N (p.Ser21Asn), rs794726902, ClinGen CA238735, cosmic curated COSV54252, ClinVar RCV000173274, CADD 22.20, PolyPhen-2 0.01, Uncertain significance, Inborn genetic diseases; not provided; Generalized epilepsy-paroxysmal dyskinesi
- S21R (p.Ser21Arg), Ensembl rs1603639328, CADD 22.70, PolyPhen-2 0.00
- S22R (p.Ser22Arg), rs2154572179, ClinGen CA377412840, ClinVar RCV002211151, Ensembl rs2154572179, CADD 22.90, PolyPhen-2 0.06, Uncertain significance, not provided
- L23H (p.Leu23His), rs1411383112, ClinGen CA377412835, ClinVar RCV003860569, TOPMed rs1411383112, CADD 27.70, PolyPhen-2 0.97, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- L23V (p.Leu23Val), TOPMed rs1207531380, gnomAD rs1207531380, CADD 26.40, PolyPhen-2 0.74
- R24G (p.Arg24Gly), TOPMed rs1350886458, gnomAD rs1350886458, CADD 24.90, PolyPhen-2 0.11, Likely benign
- R24K (p.Arg24Lys), gnomAD rs1302403980, CADD 23.60, PolyPhen-2 0.05
- R24S (p.Arg24Ser), TOPMed rs1485176204, gnomAD rs1485176204, Likely benign
- S26R (p.Ser26Arg), cosmic curated COSV99699, TOPMed rs201425608
- N28H (p.Asn28His), TOPMed rs2093893394, gnomAD rs2093893394, REVEL 0.28, CADD 26.50
- N28S (p.Asn28Ser), Ensembl rs2093893223, REVEL 0.23, CADD 23.40
- I29F (p.Ile29Phe), rs369845234, ClinGen CA5568814, ClinVar RCV003622126, 1000Genomes rs369845234, REVEL 0.44, CADD 24.60, Likely benign, Generalized epilepsy-paroxysmal dyskinesia syndrome
- I29M (p.Ile29Met), rs1186030487, ClinGen CA377412788, ClinVar RCV003510375, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- I29V (p.Ile29Val), rs369845234, ClinGen CA210159558, ClinVar RCV000701689, ClinVar RCV000730842, REVEL 0.35, CADD 23.60, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- H30Q (p.His30Gln), rs75040504, 1000Genomes rs75040504, ESP rs75040504, ExAC rs75040504, REVEL 0.28, CADD 24.20, Likely benign, Generalized epilepsy-paroxysmal dyskinesia syndrome
- H30R (p.His30Arg), rs200474297, ClinGen CA5568813, ClinVar RCV000300299, ClinVar RCV000317390, REVEL 0.35, CADD 23.80, Conflicting interpretations, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- H30Y (p.His30Tyr), rs1164839444, ClinGen CA377412787, ClinVar RCV002781507, TOPMed rs1164839444, REVEL 0.27, CADD 23.60, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A31E (p.Ala31Glu), TOPMed rs201551432, gnomAD rs201551432, REVEL 0.52, CADD 24.20, Likely benign
- A31G (p.Ala31Gly), rs201551432, ClinGen CA210159556, ClinVar RCV000698278, TOPMed rs201551432, REVEL 0.38, CADD 24.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A31P (p.Ala31Pro), rs1343575385, ClinVar RCV004572998, ClinVar RCV005100100, REVEL 0.32, CADD 25.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A31S (p.Ala31Ser), rs1343575385, ClinGen CA377412779, ClinVar RCV001216659, TOPMed rs1343575385, REVEL 0.31, CADD 23.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A31T (p.Ala31Thr), TOPMed rs1343575385, REVEL 0.35, CADD 23.40, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A31V (p.Ala31Val), rs201551432, ClinGen CA210159555, ClinVar RCV001343465, TOPMed rs201551432, REVEL 0.48, CADD 24.40, Likely benign, Generalized epilepsy-paroxysmal dyskinesia syndrome
- N32I (p.Asn32Ile), rs199570594, ClinGen CA210159553, ClinVar RCV001754074, Ensembl rs199570594, REVEL 0.41, CADD 24.40, Uncertain significance, not provided
- N32K (p.Asn32Lys), rs749212119, ClinGen CA5568812, ClinVar RCV001975693, ExAC rs749212119, REVEL 0.35, CADD 24.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- H33D (p.His33Asp), gnomAD rs2093891400, REVEL 0.27, CADD 24.00, Uncertain significance
- H33R (p.His33Arg), gnomAD rs2093891257, REVEL 0.26, CADD 23.30
- H33Y (p.His33Tyr), rs2093891400, ClinGen CA377412769, ClinVar RCV001905994, gnomAD rs2093891400, REVEL 0.34, CADD 23.80, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S35I (p.Ser35Ile), TOPMed rs988230623, gnomAD rs988230623, REVEL 0.36, CADD 24.00, Uncertain significance
- S35N (p.Ser35Asn), rs988230623, ClinGen CA377412755, ClinVar RCV003044382, TOPMed rs988230623, REVEL 0.36, CADD 23.60, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; not provided
- S35R (p.Ser35Arg), ExAC rs755591362, gnomAD rs755591362, REVEL 0.29, CADD 24.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- L36R (p.Leu36Arg), TOPMed rs2093890194
- D37N (p.Asp37Asn), Ensembl rs1603639326
- A38E (p.Ala38Glu), ESP rs375403667, ExAC rs375403667, TOPMed rs375403667, gnomAD rs375403667, REVEL 0.41, CADD 24.20
- A38G (p.Ala38Gly), ESP rs375403667, ExAC rs375403667, TOPMed rs375403667, gnomAD rs375403667, REVEL 0.33, CADD 24.50
- A38P (p.Ala38Pro), rs767099267, ClinGen CA377412738, ClinVar RCV001935416, ExAC rs767099267, REVEL 0.40, CADD 24.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A38S (p.Ala38Ser), rs767099267, ClinGen CA377412737, ClinVar RCV003329947, ClinVar RCV003777380, REVEL 0.30, CADD 23.50, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- A38T (p.Ala38Thr), rs767099267, ClinGen CA5568808, NCI-TCGA Cosmic COSV5424, cosmic curated COSV54243, REVEL 0.29, CADD 24.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A38V (p.Ala38Val), cosmic curated COSV10514, ESP rs375403667, ExAC rs375403667, TOPMed rs375403667, REVEL 0.33, CADD 24.50
- S39F (p.Ser39Phe), gnomAD rs1282366675, REVEL 0.39, CADD 24.60
- S41A (p.Ser41Ala), TOPMed rs2093888755, gnomAD rs2093888755, REVEL 0.32, CADD 24.20
- S41F (p.Ser41Phe), rs766759815, ClinGen CA5568805, ClinVar RCV001060049, ClinVar RCV001291789, REVEL 0.35, CADD 28.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; Inborn genetic diseases; Ce
- S42F (p.Ser42Phe), rs2093888082, ClinGen CA377412713, ClinVar RCV002722751, Ensembl rs2093888082, REVEL 0.12, CADD 28.30, Uncertain significance, Inborn genetic diseases
- S43F (p.Ser43Phe), Ensembl rs866492357, REVEL 0.11, CADD 24.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S43T (p.Ser43Thr), rs1057519135, ClinGen CA16043774, ClinVar RCV000416228, Ensembl rs1057519135, AlphaMissense 0.10, MetaLR 0.25, Uncertain significance, not provided
- S45F (p.Ser45Phe), gnomAD rs1429334349, REVEL 0.04, CADD 22.80
- S45T (p.Ser45Thr), Ensembl rs2093887070, REVEL 0.06, CADD 22.40
- S45Y (p.Ser45Tyr), gnomAD rs1429334349, REVEL 0.05, CADD 22.50
- S46C (p.Ser46Cys), gnomAD rs1342941141, REVEL 0.06, CADD 22.70
- S47F (p.Ser47Phe), rs907549386, ClinGen CA210159548, ClinVar RCV001912818, TOPMed rs907549386, REVEL 0.04, CADD 21.70, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S48F (p.Ser48Phe), Ensembl rs2154572147
- S49F (p.Ser49Phe), NCI-TCGA TCGA novel, REVEL 0.10, CADD 24.50, Variant assessed as somatic; moderate impact.
- S50Y (p.Ser50Tyr), NCI-TCGA Cosmic COSV5424, cosmic curated COSV54244, Variant assessed as somatic; moderate impact.
- S51F (p.Ser51Phe), rs2093884478, ClinGen CA377412663, ClinVar RCV001253510, Ensembl rs2093884478, REVEL 0.11, CADD 22.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S52F (p.Ser52Phe), rs1483499989, ClinGen CA377412658, cosmic curated COSV10879, ClinVar RCV001906031, REVEL 0.08, CADD 22.40, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S54F (p.Ser54Phe), rs765445169, ClinGen CA5568794, ClinVar RCV003857365, ExAC rs765445169, REVEL 0.07, CADD 23.80, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- S56F (p.Ser56Phe), NCI-TCGA TCGA novel, Ensembl rs2154572142, Variant assessed as somatic; moderate impact.
- S57F (p.Ser57Phe), TOPMed rs1394425026, REVEL 0.11, CADD 25.20
- S58* (p.Ser58Ter), ExAC rs776719617, TOPMed rs776719617, gnomAD rs776719617, Uncertain significance
- S58L (p.Ser58Leu), rs776719617, ClinGen CA5568791, ClinVar RCV001214218, ClinVar RCV005348358, REVEL 0.09, CADD 26.80, Uncertain significance, Inborn genetic diseases; Generalized epilepsy-paroxysmal dyskinesia syndrome
- S59P (p.Ser59Pro), rs2093880726, ClinGen CA377412620, ClinVar RCV001757836, ClinVar RCV001882825, CADD 14.80, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- S59F (p.Ser59Phe), rs2552275366, ClinGen CA377412616, ClinVar RCV003623854, ClinVar RCV005860386, REVEL 0.12, CADD 25.70, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; Liang-Wang syndrome
- S60* (p.Ser60Ter), ExAC rs768769748, TOPMed rs768769748, gnomAD rs768769748, Benign
- S60L (p.Ser60Leu), rs768769748, ClinGen CA5568790, ClinVar RCV001906338, ClinVar RCV002246584, REVEL 0.03, CADD 23.00, Conflicting interpretations, Inborn genetic diseases; Generalized epilepsy-paroxysmal dyskinesia syndrome; no
- S60W (p.Ser60Trp), rs768769748, ClinGen CA377412612, ClinVar RCV000799033, ExAC rs768769748, REVEL 0.14, CADD 27.00, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- V61A (p.Val61Ala), rs200420124, ClinGen CA5568787, ClinVar RCV000287363, ClinVar RCV001557104, REVEL 0.07, CADD 24.80, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome; Cerebellar at
- V61I (p.Val61Ile), gnomAD rs1210717644, REVEL 0.12, CADD 21.30
- H62Q (p.His62Gln), rs974972197, ClinGen CA210159544, ClinVar RCV003072587, TOPMed rs974972197, REVEL 0.05, CADD 22.60, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- E63Q (p.Glu63Gln), rs749265202, ClinGen CA5568786, ClinVar RCV000803660, ClinVar RCV004629335, REVEL 0.05, CADD 22.20, Conflicting interpretations, Generalized epilepsy-paroxysmal dyskinesia syndrome; Cerebellar atrophy, develop
- P64R (p.Pro64Arg), gnomAD rs1207714308, REVEL 0.12, CADD 24.80
- K65N (p.Lys65Asn), gnomAD rs1301827200, REVEL 0.08, CADD 22.80
- D67G (p.Asp67Gly), gnomAD rs1213908683
- D67N (p.Asp67Asn), cosmic curated COSV10727, Ensembl rs2154572136
- A68V (p.Ala68Val), NCI-TCGA Cosmic COSV5426, cosmic curated COSV54260, CADD 15.90, Variant assessed as somatic; moderate impact.
- I70M (p.Ile70Met), TOPMed rs1435246496, gnomAD rs1435246496, REVEL 0.13, CADD 23.20
- I71N (p.Ile71Asn), TOPMed rs1404837982, gnomAD rs1404837982, REVEL 0.22, CADD 29.70
- I71T (p.Ile71Thr), cosmic curated COSV54294, TOPMed rs1404837982, gnomAD rs1404837982, REVEL 0.29, CADD 23.40
- I71V (p.Ile71Val), rs2552275339, ClinGen CA377412541, ClinVar RCV003881185, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- P72R (p.Pro72Arg), rs2093876319, ClinGen CA377412531, ClinVar RCV001217379, Ensembl rs2093876319, AlphaMissense 0.92, MetaLR 0.14, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- M75I (p.Met75Ile), rs1464796627, ClinGen CA377412510, ClinVar RCV001918058, ClinVar RCV005350727, REVEL 0.08, CADD 22.10, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; Inborn genetic diseases
- P78L (p.Pro78Leu), rs1760330958, ClinGen CA377412488, cosmic curated COSV54256, ClinVar RCV003031510, REVEL 0.28, CADD 23.60, Uncertain significance, Inborn genetic diseases; Generalized epilepsy-paroxysmal dyskinesia syndrome
- P78S (p.Pro78Ser), TOPMed rs1347749251, gnomAD rs1347749251, REVEL 0.24, CADD 23.10
- C79W (p.Cys79Trp), rs2154572129, ClinGen CA377412480, ClinVar RCV001755015, Ensembl rs2154572129, AlphaMissense 1.00, MetaLR 0.18, Uncertain significance, not provided
- R82Q (p.Arg82Gln), TOPMed rs1361269831, gnomAD rs1361269831, REVEL 0.04, CADD 22.90
- G83D (p.Gly83Asp), NCI-TCGA Cosmic COSV9969, cosmic curated COSV99698, Variant assessed as somatic; moderate impact.
- R85S (p.Arg85Ser), rs2154572127, ClinGen CA377412444, ClinVar RCV001910312, Ensembl rs2154572127, AlphaMissense 1.00, MetaLR 0.25, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- M86L (p.Met86Leu), ExAC rs754652887, gnomAD rs754652887, REVEL 0.22, CADD 20.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- A89S (p.Ala89Ser), ExAC rs751208535, gnomAD rs751208535, CADD 5.81
- A89V (p.Ala89Val), ExAC rs780328891, gnomAD rs780328891, REVEL 0.09, CADD 24.70
- F90I (p.Phe90Ile), NCI-TCGA Cosmic COSV9969, cosmic curated COSV99699, Variant assessed as somatic; moderate impact.
- F90V (p.Phe90Val), ExAC rs758802212, gnomAD rs758802212
- A92V (p.Ala92Val), ExAC rs765858133, gnomAD rs765858133, REVEL 0.29, CADD 23.70
- S93F (p.Ser93Phe), rs2552275315, ClinGen CA377412386, ClinVar RCV003510364, ClinVar RCV005241540, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- S94A (p.Ser94Ala), rs2552275312, ClinGen CA377412383, ClinVar RCV003127239, Uncertain significance, Autism spectrum disorder
- S94F (p.Ser94Phe), cosmic curated COSV10582, NCI-TCGA Cosmic COSV9969, REVEL 0.36, CADD 31.00, Variant assessed as somatic; moderate impact.
- S94Y (p.Ser94Tyr), NCI-TCGA Cosmic COSV9969, cosmic curated COSV99698, Variant assessed as somatic; moderate impact.
- M95I (p.Met95Ile), TOPMed rs202167200
- M95L (p.Met95Leu), ExAC rs762347754, TOPMed rs762347754, gnomAD rs762347754, REVEL 0.16, AlphaMissense 0.59, Uncertain significance
- M95V (p.Met95Val), rs762347754, ClinGen CA377412379, ClinVar RCV001322342, ClinVar RCV004584882, AlphaMissense 0.59, MetaLR 0.06, Uncertain significance, not provided; Generalized epilepsy-paroxysmal dyskinesia syndrome
- V96A (p.Val96Ala), NCI-TCGA Cosmic COSV5423, cosmic curated COSV54237, Uncertain significance, not provided
- T97S (p.Thr97Ser), Ensembl rs1603639322, REVEL 0.14, CADD 29.50
- F98L (p.Phe98Leu), NCI-TCGA Cosmic COSV9970, cosmic curated COSV99700, Variant assessed as somatic; moderate impact.
- G100R (p.Gly100Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- L102F (p.Leu102Phe), TOPMed rs2093872226
- F103Y (p.Phe103Tyr), NCI-TCGA Cosmic COSV5423, cosmic curated COSV54234, Variant assessed as somatic; moderate impact.
- I104V (p.Ile104Val), rs2552275301, ClinGen CA377412317, ClinVar RCV003271250, Uncertain significance, Inborn genetic diseases
- I105L (p.Ile105Leu), gnomAD rs200933516, REVEL 0.11, CADD 24.10
- I105V (p.Ile105Val), gnomAD rs200933516
- L107F (p.Leu107Phe), rs2552275299, ClinGen CA377412296, ClinVar RCV002818655, REVEL 0.08, CADD 24.10, Uncertain significance, Inborn genetic diseases
- L107H (p.Leu107His), rs2552275298, ClinGen CA377412295, ClinVar RCV003622599, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- W108* (p.Trp108Ter), NCI-TCGA Cosmic COSV5425, cosmic curated COSV54250, Variant assessed as somatic; high impact.
- R109W (p.Arg109Trp), rs1303770190, NCI-TCGA Cosmic COSV9969, cosmic curated COSV99699, gnomAD rs1303770190, AlphaMissense 1.00, MetaLR 0.23, Variant assessed as somatic; moderate impact.
- T110M (p.Thr110Met), ExAC rs772934866, gnomAD rs772934866, REVEL 0.30, CADD 24.70
- L111F (p.Leu111Phe), Ensembl rs2154572109
- K112E (p.Lys112Glu), rs769727956, ClinGen CA5568767, ClinVar RCV003621955, ExAC rs769727956, REVEL 0.30, CADD 23.40, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- K112N (p.Lys112Asn), rs748112495, ClinGen CA377412261, ClinVar RCV001977743, ExAC rs748112495, AlphaMissense 0.78, MetaLR 0.09, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- K112R (p.Lys112Arg), gnomAD rs1430426336, REVEL 0.24, CADD 24.60
- L114M (p.Leu114Met), rs780623276, ClinGen CA5568765, cosmic curated COSV54224, ClinVar RCV000813847, REVEL 0.14, CADD 23.40, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- W115C (p.Trp115Cys), gnomAD rs1235134297, REVEL 0.31, CADD 25.50
- V117L (p.Val117Leu), rs1257184004, ClinGen CA377412232, ClinVar RCV002295099, TOPMed rs1257184004, AlphaMissense 0.80, MetaLR 0.11, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- V117M (p.Val117Met), rs1257184004, ClinGen CA377412233, ClinVar RCV001360178, TOPMed rs1257184004, REVEL 0.24, AlphaMissense 0.80, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- C118G (p.Cys118Gly), rs2154572103, ClinGen CA377412225, ClinVar RCV002031894, Ensembl rs2154572103, AlphaMissense 0.92, MetaLR 0.25, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- H120N (p.His120Asn), NCI-TCGA Cosmic COSV9969, cosmic curated COSV99699, Variant assessed as somatic; moderate impact.
- H120Q (p.His120Gln), ESP rs147098205, REVEL 0.19, CADD 23.10
- H120Y (p.His120Tyr), rs2552275283, ClinGen CA377412209, ClinVar RCV003131318, Uncertain significance, not provided
- C121F (p.Cys121Phe), rs2154572100, ClinGen CA2573146002, ClinVar RCV001921451, Ensembl rs2154572100, REVEL 0.31, CADD 24.10, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- C121G (p.Cys121Gly), TOPMed rs1390486916, Uncertain significance
- C121R (p.Cys121Arg), rs1390486916, ClinGen CA377412204, ClinVar RCV001341922, TOPMed rs1390486916, AlphaMissense 0.91, MetaLR 0.12, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G122A (p.Gly122Ala), rs199568153, ClinGen CA5568761, ClinVar RCV001303799, ClinVar RCV001732119, REVEL 0.09, CADD 20.60, Uncertain significance, Cerebellar atrophy, developmental delay, and seizures; Inborn genetic diseases
- G122R (p.Gly122Arg), rs1167824169, ClinGen CA377412196, cosmic curated COSV10514, ClinVar RCV002043934, REVEL 0.11, CADD 22.60, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- G123D (p.Gly123Asp), rs2093865429, ClinGen CA377412186, cosmic curated COSV99694, ClinVar RCV001323888, REVEL 0.23, CADD 22.10, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; not provided
- G123R (p.Gly123Arg), gnomAD rs1246413912, Uncertain significance
- G123S (p.Gly123Ser), rs1246413912, ClinGen CA377412191, NCI-TCGA Cosmic COSV5427, cosmic curated COSV54275, REVEL 0.20, CADD 22.30, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- K124N (p.Lys124Asn), gnomAD rs1305892021
- K124R (p.Lys124Arg), ExAC rs750826732, gnomAD rs750826732, REVEL 0.29, CADD 23.40
- T125A (p.Thr125Ala), ExAC rs779419680, gnomAD rs779419680, REVEL 0.04, CADD 21.10
- T125M (p.Thr125Met), rs2154572092, ClinGen CA377412174, ClinVar RCV001863582, Ensembl rs2154572092, REVEL 0.11, CADD 23.20, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
- T125S (p.Thr125Ser), ExAC rs779419680, gnomAD rs779419680
- A128T (p.Ala128Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A128V (p.Ala128Val), TOPMed rs1409273798, gnomAD rs1409273798
- Q129E (p.Gln129Glu), rs377430922, ClinGen CA210133345, ClinVar RCV001296424, ClinVar RCV005408818, REVEL 0.14, CADD 17.60, Uncertain significance, not specified; Generalized epilepsy-paroxysmal dyskinesia syndrome
- Q129K (p.Gln129Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q129R (p.Gln129Arg), ExAC rs763787979, gnomAD rs763787979, REVEL 0.10, CADD 21.90
- K130N (p.Lys130Asn), NCI-TCGA Cosmic COSV9969, cosmic curated COSV99699, Variant assessed as somatic; moderate impact.
- K130R (p.Lys130Arg), rs138918358, ClinGen CA5568710, ClinVar RCV003861468, ClinVar RCV004767499, REVEL 0.06, CADD 21.90, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome; not provided
- I131F (p.Ile131Phe), 1000Genomes rs541069424, ExAC rs541069424, TOPMed rs541069424, gnomAD rs541069424, REVEL 0.14, CADD 20.90
- I131T (p.Ile131Thr), Ensembl rs957532714, REVEL 0.18, CADD 21.30
- I131V (p.Ile131Val), 1000Genomes rs541069424, ExAC rs541069424, TOPMed rs541069424, gnomAD rs541069424, REVEL 0.06, CADD 17.50
- N132H (p.Asn132His), TOPMed rs1033528866, Uncertain significance, Generalized epilepsy-paroxysmal dyskinesia syndrome
Public KCNMA1 analysis runs
- KCNMA1 analysis run — KCNMA1 (1,392 variants) — completed 2026-08-19