SCN1A (Nav1.1) variants and mutations
SCN1A (also known as Nav1.1) is a human protein-coding gene encoding a sodium channel protein type 1 subunit alpha protein. Its sodium current is especially important for reliable firing of inhibitory interneurons and therefore for balancing excitation across neural networks. Loss-of-function variants are the major cause of Dravet syndrome, while other variants cause GEFS+ or familial hemiplegic migraine. This analysis covers 3,810 SCN1A variants and mutations. Of these, 79% have computational variant effect predictions. Disease context includes Dravet syndrome, generalized epilepsy with febrile seizures plus, type 2, and Generalized epilepsy with febrile seizures-plus. Example SCN1A variants include M1?, E2D, and Q3K.
Variant analysis overview
- Gene: SCN1A
- Protein: Nav1.1
- UniProt accession: P35498
- Organism: Homo sapiens
- Variants analyzed: 3810
- Variant scope: all variants
- Completed: 2026-08-09
Variant and mutation evidence
- Variant composition: 3,406 unspecified-consequence records; 206 synonymous variants; 172 missense variants; 14 frameshift variants; 1 in-frame deletions; 1 in-frame insertions; 1 stop retained variant; 2 stop lost; 4 stop-gained variants; 1 splice-region variants; 2 substitution
- Prediction scores: 3,015 variants have prediction scores (79% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Dravet syndrome, generalized epilepsy with febrile seizures plus, type 2, Generalized epilepsy with febrile seizures-plus, epilepsy, migraine, familial hemiplegic, 3, genetic developmental and epileptic encephalopathy, Seizure, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalo, Lennox-Gastaut syndrome, febrile seizures, familial, 3a, focal epilepsy, familial or sporadic hemiplegic migraine.
Protein structure and variant hotspots
- Protein features: 24 transmembrane segments; 1 domains; 17 post-translational modification sites.
- Structural context: 1,099 variants have structural context.
- PTM context: 21 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.
Diseases linked to SCN1A
- Developmental and epileptic encephalopathy genes and variants
- Early-infantile DEE genes and variants
- Severe myoclonic epilepsy in infancy genes and variants
- Amyotrophic lateral sclerosis genes and variants
- Generalized epilepsy with febrile seizures plus genes and variants
- Familial hemiplegic migraine genes and variants
- Cardiac arrhythmia genes and variants
- Familial febrile seizures genes and variants
- Epilepsy genes and variants
- Autosomal dominant epilepsy genes and variants
- Focal epilepsy genes and variants
- Migraine genes and variants
Notable SCN1A variants
Examples include M1?, E2D, Q3K, T4I, V5M, L6F, L6R, V7I. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, NCI-TCGA Cosmic COSV1003, cosmic curated COSV10031, Variant assessed as somatic; high impact.
- E2D (p.Glu2Asp), rs771003075, ClinGen CA349243508, ClinVar RCV001806592, ExAC rs771003075, AlphaMissense 0.15, MetaLR 0.79, Uncertain significance, not provided
- Q3K (p.Gln3Lys), rs924198007, ClinGen CA60270536, ClinVar RCV006468361, TOPMed rs924198007, CADD 23.60, PolyPhen-2 0.72, Uncertain significance, Early-infantile DEE
- T4I (p.Thr4Ile), rs374317182, ClinGen CA1943575, cosmic curated COSV57666, ClinVar RCV006563846, CADD 23.20, PolyPhen-2 0.05, Uncertain significance, Early-infantile DEE
- V5M (p.Val5Met), gnomAD rs1684709924, CADD 22.90
- L6F (p.Leu6Phe), gnomAD rs1684709579, CADD 25.80, PolyPhen-2 0.99
- L6R (p.Leu6Arg), TOPMed rs1684709117, gnomAD rs1684709117, CADD 26.40
- V7I (p.Val7Ile), Ensembl rs1684708436
- P8L (p.Pro8Leu), rs1365133608, ClinGen CA349243472, ClinVar RCV003235841, TOPMed rs1365133608, CADD 27.30, PolyPhen-2 1.00, Uncertain significance, not provided
- P8T (p.Pro8Thr), gnomAD rs1400870623, CADD 25.60, PolyPhen-2 1.00
- P9A (p.Pro9Ala), rs757688309, ClinGen CA60270535, ClinVar RCV006465228, TOPMed rs757688309, AlphaMissense 0.24, MetaLR 0.88, Uncertain significance, Early-infantile DEE
- P9T (p.Pro9Thr), rs757688309, ClinGen CA349243470, ClinVar RCV003110097, TOPMed rs757688309, AlphaMissense 0.24, MetaLR 0.88, Uncertain significance, not provided
- G10* (p.Gly10Ter), gnomAD rs1459246073
- G10R (p.Gly10Arg), gnomAD rs1459246073, CADD 25.70, PolyPhen-2 1.00
- G10V (p.Gly10Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P11H (p.Pro11His), rs1350460260, ClinGen CA349243456, ClinVar RCV001355130, ClinVar RCV006606844, CADD 26.00, PolyPhen-2 1.00, Uncertain significance, Early-infantile DEE
- P11L (p.Pro11Leu), TOPMed rs1350460260, gnomAD rs1350460260, CADD 26.60, Uncertain significance
- P11S (p.Pro11Ser), rs1684706255, ClinGen CA349243458, ClinVar RCV006465134, Ensembl rs1684706255, AlphaMissense 0.32, MetaLR 0.89, Uncertain significance, Early-infantile DEE
- P11T (p.Pro11Thr), Ensembl rs1684706255, Uncertain significance
- D12E (p.Asp12Glu), TOPMed rs911813526, gnomAD rs911813526, Uncertain significance, not provided
- D12Y (p.Asp12Tyr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S13I (p.Ser13Ile), rs1684704155, ClinGen CA349243442, ClinVar RCV002243593, Ensembl rs1684704155, CADD 25.60, PolyPhen-2 0.98, Uncertain significance, Severe myoclonic epilepsy in infancy
- S13N (p.Ser13Asn), Ensembl rs1684704155, CADD 23.00, Uncertain significance
- F14L (p.Phe14Leu), Ensembl rs367837716
- R19* (p.Arg19Ter), gnomAD rs796053096, Uncertain significance
- R19G (p.Arg19Gly), rs796053096, ClinGen CA317796, ClinVar RCV000189087, gnomAD rs796053096, AlphaMissense 0.19, MetaLR 0.89, Uncertain significance, not provided
- R19K (p.Arg19Lys), rs1479913332, ClinGen CA349243399, ClinVar RCV006606466, TOPMed rs1479913332, CADD 17.80, PolyPhen-2 0.00, Uncertain significance, Early-infantile DEE
- E20* (p.Glu20Ter), cosmic curated COSV10032, Ensembl rs1553560946
- E20D (p.Glu20Asp), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10032, Variant assessed as somatic; moderate impact.
- L22F (p.Leu22Phe), NCI-TCGA Cosmic COSV5768, cosmic curated COSV57688, Variant assessed as somatic; moderate impact.
- A23E (p.Ala23Glu), rs139397227, ClinGen CA317363, cosmic curated COSV57661, ClinVar RCV000188916, CADD 24.50, PolyPhen-2 0.67, Uncertain significance, Early-infantile DEE; Inborn genetic diseases; not provided
- A23V (p.Ala23Val), rs139397227, ClinGen CA317367, ClinVar RCV000188917, ClinVar RCV000534453, CADD 23.50, PolyPhen-2 0.96, Benign/Likely benign, not specified; Early-infantile DEE; Inborn genetic diseases
- A24G (p.Ala24Gly), rs1489662325, ClinGen CA349243351, ClinVar RCV005271220, ClinVar RCV006466758, CADD 26.00, PolyPhen-2 0.97, Uncertain significance, Early-infantile DEE; Inborn genetic diseases
- A24T (p.Ala24Thr), rs794726848, ClinGen CA303581, ClinVar RCV000180979, Ensembl rs794726848, AlphaMissense 0.10, MetaLR 0.83, Pathogenic, Severe myoclonic epilepsy in infancy
- A24V (p.Ala24Val), NCI-TCGA Cosmic COSV5767, cosmic curated COSV57671, Variant assessed as somatic; moderate impact.
- I25F (p.Ile25Phe), rs2105983873, ClinGen CA349243341, ClinVar RCV002244425, Ensembl rs2105983873, AlphaMissense 0.62, MetaLR 0.97, Uncertain significance, not provided
- I25T (p.Ile25Thr), TOPMed rs1684699254, gnomAD rs1684699254, CADD 26.00, PolyPhen-2 0.97, Uncertain significance, not provided
- E26* (p.Glu26Ter), rs76921794, ClinGen CA60270532, ClinVar RCV005253949, ClinVar RCV006468550, CADD 36.00, Pathogenic
- R27* (p.Arg27Ter), Ensembl rs1553560926
- R27T (p.Arg27Thr), rs121917906, ClinGen CA266095, ClinVar RCV000059458, ClinVar RCV000585038, CADD 23.00, PolyPhen-2 0.01, Conflicting interpretations, Early-infantile DEE; Inborn genetic diseases; not provided
- R28C (p.Arg28Cys), rs754032480, ClinGen CA317371, cosmic curated COSV57691, ClinVar RCV000188919, CADD 29.60, PolyPhen-2 1.00, Conflicting interpretations, Migraine, familial hemiplegic, 3; Developmental and epileptic encephalopathy 6B
- R28H (p.Arg28His), rs398123601, ClinGen CA221620, NCI-TCGA Cosmic COSV1003, cosmic curated COSV10031, CADD 27.00, PolyPhen-2 0.99, Likely benign, Generalized epilepsy with febrile seizures plus
- I29T (p.Ile29Thr), rs773935383, ClinGen CA60270531, ClinVar RCV001760997, ClinVar RCV006467867, AlphaMissense 0.22, MetaLR 0.92, Uncertain significance, Early-infantile DEE; not provided
- A30T (p.Ala30Thr), gnomAD rs1299450103
- E31* (p.Glu31Ter), gnomAD rs1368004941
- E31D (p.Glu31Asp), Ensembl rs1684693841, CADD 20.60, PolyPhen-2 0.05
- E31K (p.Glu31Lys), gnomAD rs1368004941, CADD 22.80, PolyPhen-2 0.10
- E32* (p.Glu32Ter), cosmic curated COSV57689, Ensembl rs1553560889
- K33* (p.Lys33Ter), ESP rs375913842, TOPMed rs375913842, gnomAD rs375913842, Uncertain significance
- K33E (p.Lys33Glu), rs375913842, ClinGen CA60270530, ClinVar RCV004960816, ClinVar RCV006557387, CADD 24.20, PolyPhen-2 0.98, Uncertain significance, Early-infantile DEE; Inborn genetic diseases
- K33M (p.Lys33Met), NCI-TCGA Cosmic COSV5767, Variant assessed as somatic; moderate impact.
- A34G (p.Ala34Gly), Ensembl rs1559284943, CADD 25.70, PolyPhen-2 0.94, Uncertain significance, not provided
- A34P (p.Ala34Pro), ExAC rs765678699, gnomAD rs765678699, CADD 25.20, PolyPhen-2 0.98
- K35* (p.Lys35Ter), Ensembl rs1553560861
- K35N (p.Lys35Asn), NCI-TCGA TCGA novel, 1000Genomes rs41265141, ExAC rs41265141, gnomAD rs41265141, Variant assessed as somatic; moderate impact.
- N36T (p.Asn36Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- P37H (p.Pro37His), TOPMed rs963757668, Uncertain significance, Inborn genetic diseases; Early-infantile DEE
- P37L (p.Pro37Leu), NCI-TCGA TCGA novel, TOPMed rs963757668, Uncertain significance
- P37S (p.Pro37Ser), rs1468825512, NCI-TCGA Cosmic COSV5766, cosmic curated COSV57661, gnomAD rs1468825512, CADD 20.20, PolyPhen-2 0.00, Likely benign
- P37T (p.Pro37Thr), rs1468825512, ClinGen CA349243188, ClinVar RCV006377219, ClinVar RCV006466923, CADD 21.20, PolyPhen-2 0.05, Conflicting interpretations, Early-infantile DEE; Inborn genetic diseases
- K38* (p.Lys38Ter), Ensembl rs1553560846
- P39A (p.Pro39Ala), cosmic curated COSV57672, TOPMed rs968754992, gnomAD rs968754992, CADD 16.90, PolyPhen-2 0.01, Uncertain significance
- P39T (p.Pro39Thr), rs968754992, ClinGen CA60270528, ClinVar RCV006465955, TOPMed rs968754992, CADD 19.30, PolyPhen-2 0.04, Uncertain significance, Early-infantile DEE
- D40G (p.Asp40Gly), rs1684688433, ClinGen CA349243156, ClinVar RCV005271134, ClinVar RCV005415612, CADD 22.80, PolyPhen-2 0.17, Conflicting interpretations, Inborn genetic diseases; Early-infantile DEE; not provided
- D40N (p.Asp40Asn), rs1574373061, ClinGen CA349243162, ClinVar RCV004719990, ClinVar RCV006464264, AlphaMissense 0.08, MetaLR 0.84, Conflicting interpretations, Early-infantile DEE; not provided
- K41* (p.Lys41Ter), rs764444350, ClinGen CA303232, ClinVar RCV000180846, ExAC rs764444350, AlphaMissense 0.10, MetaLR 0.77, Pathogenic
- K41E (p.Lys41Glu), rs764444350, ClinGen CA1943567, ClinVar RCV001763063, ExAC rs764444350, AlphaMissense 0.10, MetaLR 0.77, Uncertain significance, not provided
- K41N (p.Lys41Asn), TOPMed rs1276806499, CADD 16.60, PolyPhen-2 0.04
- K42* (p.Lys42Ter), Ensembl rs1553560836
- K42N (p.Lys42Asn), NCI-TCGA Cosmic COSV5766, cosmic curated COSV57663, Variant assessed as somatic; moderate impact.
- K42T (p.Lys42Thr), rs760777182, ClinGen CA1943566, cosmic curated COSV57660, ClinVar RCV006468262, CADD 23.30, PolyPhen-2 0.96, Uncertain significance, Early-infantile DEE
- D43N (p.Asp43Asn), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10031, Variant assessed as somatic; moderate impact.
- D43R (p.Asp43Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- D45E (p.Asp45Glu), rs201985242, ClinGen CA1943563, ClinVar RCV006463745, 1000Genomes rs201985242, CADD 0.00, PolyPhen-2 0.65, Likely benign, Early-infantile DEE
- D45G (p.Asp45Gly), rs1559284606, ClinGen CA349243095, ClinVar RCV000729035, ClinVar RCV006608040, AlphaMissense 0.12, MetaLR 0.88, Uncertain significance, Early-infantile DEE; not provided
- D45N (p.Asp45Asn), rs531894715, NCI-TCGA Cosmic COSV5767, cosmic curated COSV57674, UniProt VAR 073442, CADD 23.00, PolyPhen-2 0.98, Uncertain significance
- E46* (p.Glu46Ter), ExAC rs769582667, TOPMed rs769582667, gnomAD rs769582667, Uncertain significance
- E46G (p.Glu46Gly), gnomAD rs1344895276, CADD 26.70
- E46K (p.Glu46Lys), rs769582667, ClinGen CA1943562, NCI-TCGA Cosmic COSV5766, cosmic curated COSV57660, CADD 23.00, PolyPhen-2 0.96, Uncertain significance, not provided; Early-infantile DEE; Generalized epilepsy with febrile seizures pl
- N47S (p.Asn47Ser), rs1296134461, ClinGen CA349243068, ClinVar RCV004066013, ClinVar RCV006611990, CADD 18.30, PolyPhen-2 0.19, Uncertain significance, Inborn genetic diseases; Early-infantile DEE
- G48C (p.Gly48Cys), NCI-TCGA Cosmic COSV5767, cosmic curated COSV57674, Variant assessed as somatic; moderate impact.
- K50* (p.Lys50Ter), Ensembl rs1553560800
- P51T (p.Pro51Thr), TOPMed rs1684680324
- S53I (p.Ser53Ile), NCI-TCGA Cosmic COSV1003, cosmic curated COSV10032, Variant assessed as somatic; moderate impact.
- S53N (p.Ser53Asn), gnomAD rs1199414919, CADD 22.90, PolyPhen-2 0.52
- L55* (p.Leu55Ter), Ensembl rs1553560791
- E56* (p.Glu56Ter), Ensembl rs1553560788
- E56K (p.Glu56Lys), Ensembl rs1553560788
- A57G (p.Ala57Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A57S (p.Ala57Ser), cosmic curated COSV57681, ExAC rs747925160, gnomAD rs747925160
- A57T (p.Ala57Thr), ExAC rs747925160, gnomAD rs747925160, CADD 26.10, PolyPhen-2 0.99
- G58* (p.Gly58Ter), Ensembl rs1553560785, Pathogenic, in DRVT
- G58R (p.Gly58Arg), rs1553560785, ClinGen CA349242943, ClinVar RCV006466818, Ensembl rs1553560785, AlphaMissense 0.97, MetaLR 0.96, Pathogenic, Early-infantile DEE
- G58V (p.Gly58Val), UniProt VAR 073443, Likely pathogenic, Severe myoclonic epilepsy in infancy
- K59* (p.Lys59Ter), Ensembl rs1553560783
- K59N (p.Lys59Asn), ExAC rs776279313, gnomAD rs776279313, CADD 23.00, PolyPhen-2 0.98
- K59R (p.Lys59Arg), gnomAD rs1684677001, CADD 23.70
- N60K (p.Asn60Lys), ExAC rs746510690, TOPMed rs746510690, gnomAD rs746510690, CADD 16.00, PolyPhen-2 0.01, Likely benign
- N60T (p.Asn60Thr), Ensembl rs1684675908
- N60Y (p.Asn60Tyr), ExAC rs768312630, gnomAD rs768312630, CADD 23.30, PolyPhen-2 0.12
- L61F (p.Leu61Phe), rs2105982797, ClinGen CA349242906, ClinVar RCV006468595, Ensembl rs2105982797, AlphaMissense 0.90, MetaLR 0.98, Pathogenic, Early-infantile DEE
- L61P (p.Leu61Pro), rs1553560766, ClinGen CA317800, ClinVar RCV001787423, Ensembl rs1553560766, AlphaMissense 0.99, MetaLR 0.97, Likely pathogenic, Sudden unexplained death in childhood
- F63L (p.Phe63Leu), rs121917907, ClinGen CA284883, ClinVar RCV000059385, ClinVar RCV006555395, CADD 23.90, PolyPhen-2 0.97, Uncertain significance, Early-infantile DEE
- Y65* (p.Tyr65Ter), rs1684672231, ClinGen CA349242852, ClinVar RCV002250326, TOPMed rs1684672231, Pathogenic
- G66S (p.Gly66Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- G66V (p.Gly66Val), NCI-TCGA Cosmic COSV5768, Variant assessed as somatic; moderate impact.
- D67V (p.Asp67Val), rs2105982601, ClinGen CA349242835, ClinVar RCV001755096, Ensembl rs2105982601, AlphaMissense 0.76, MetaLR 0.94, Uncertain significance, not provided
- I68S (p.Ile68Ser), rs758871507, ClinGen CA317804, ClinVar RCV000189089, ClinVar RCV006461937, AlphaMissense 0.38, MetaLR 0.91, Likely pathogenic, not provided; Early-infantile DEE
- I68T (p.Ile68Thr), rs758871507, ClinGen CA1943556, ClinVar RCV000781834, ClinVar RCV001759474, AlphaMissense 0.38, MetaLR 0.91, Uncertain significance, Intellectual disability
- P69A (p.Pro69Ala), Ensembl rs1684670553
- P69L (p.Pro69Leu), Ensembl rs1684670190, CADD 27.70, PolyPhen-2 1.00
- P70T (p.Pro70Thr), rs2105982466, ClinGen CA349242808, ClinVar RCV006557989, Ensembl rs2105982466, AlphaMissense 0.09, MetaLR 0.90, Uncertain significance, Early-infantile DEE
- M72I (p.Met72Ile), NCI-TCGA Cosmic COSV5766, cosmic curated COSV57667, Variant assessed as somatic; moderate impact.
- V73A (p.Val73Ala), TOPMed rs1684668753, Uncertain significance, Early-infantile DEE
- V73L (p.Val73Leu), TOPMed rs201229812, CADD 23.50, PolyPhen-2 0.96, Uncertain significance, Early-infantile DEE; not provided
- S74* (p.Ser74Ter), NCI-TCGA Cosmic COSV5765, cosmic curated COSV57659, Uncertain significance, in GEFSP2
- S74P (p.Ser74Pro), rs121917931, ClinGen CA266089, ClinVar RCV000059386, ClinVar RCV006461355, AlphaMissense 0.96, MetaLR 0.94, Pathogenic, Early-infantile DEE
- E75* (p.Glu75Ter), Ensembl rs1553560731
- P76L (p.Pro76Leu), gnomAD rs1399391997, CADD 27.20, PolyPhen-2 1.00, Likely pathogenic, Early-infantile DEE
- P76S (p.Pro76Ser), rs1574371737, ClinGen CA349242740, ClinVar RCV006464348, Ensembl rs1574371737, AlphaMissense 0.87, MetaLR 0.97, Likely pathogenic, Early-infantile DEE
- L77P (p.Leu77Pro), rs2105982276, ClinGen CA349242727, ClinVar RCV002449505, ClinVar RCV006468228, AlphaMissense 1.00, MetaLR 0.98, Pathogenic/Likely pathogenic, Early-infantile DEE; Inborn genetic diseases
- E78* (p.Glu78Ter), Ensembl rs1553560710
- E78D (p.Glu78Asp), rs121917933, ClinGen CA284889, ClinVar RCV000059388, UniProt VAR 029660, AlphaMissense 0.67, MetaLR 0.96, not provided, in DRVT
- D79E (p.Asp79Glu), rs1276982403, ClinGen CA349242702, ClinVar RCV006563858, TOPMed rs1276982403, CADD 23.90, PolyPhen-2 0.99, Likely pathogenic, Early-infantile DEE
- D79H (p.Asp79His), rs121917982, ClinGen CA284892, ClinVar RCV000059389, UniProt VAR 064346, AlphaMissense 1.00, MetaLR 0.98, not provided, Severe myoclonic epilepsy in infancy
- D79N (p.Asp79Asn), rs121917982, ClinGen CA16604053, ClinVar RCV000419539, UniProt VAR 073446, AlphaMissense 1.00, MetaLR 0.98, Pathogenic, not provided
- L80V (p.Leu80Val), rs2105982158, ClinGen CA349242699, ClinVar RCV006377146, ClinVar RCV006466701, CADD 22.70, PolyPhen-2 0.22, Uncertain significance, Early-infantile DEE; Inborn genetic diseases
- D81E (p.Asp81Glu), rs796053016, ClinGen CA349242681, ClinVar RCV006466836, Ensembl rs796053016, AlphaMissense 0.98, MetaLR 0.95, Pathogenic, Early-infantile DEE
- D81G (p.Asp81Gly), rs1684663181, ClinGen CA349242686, ClinVar RCV001030755, ClinVar RCV006465079, AlphaMissense 0.99, MetaLR 0.98, Conflicting interpretations, Severe myoclonic epilepsy in infancy; Generalized epilepsy with febrile seizures
- P82L (p.Pro82Leu), rs2105982111, ClinGen CA349242671, ClinVar RCV005626534, ClinVar RCV006557973, AlphaMissense 0.29, MetaLR 0.94, Conflicting interpretations, not provided; Early-infantile DEE
- Y83* (p.Tyr83Ter), rs863225031, ClinGen CA325464, ClinVar RCV000201161, ClinVar RCV006555663, Pathogenic
- Y83C (p.Tyr83Cys), rs1574371399, ClinGen CA349242664, cosmic curated COSV57685, ClinVar RCV006464288, AlphaMissense 0.46, MetaLR 0.95, Pathogenic, Early-infantile DEE
- Y83D (p.Tyr83Asp), rs1362796016, ClinGen CA349242667, ClinVar RCV006468611, gnomAD rs1362796016, AlphaMissense 0.59, MetaLR 0.96, Pathogenic, Early-infantile DEE
- Y83H (p.Tyr83His), gnomAD rs1362796016, AlphaMissense 0.59, MetaLR 0.96, Pathogenic
- Y84* (p.Tyr84Ter), rs2105982029, ClinGen CA349242651, ClinVar RCV001388200, ClinVar RCV003311984, Pathogenic, in DRVT
- Y84C (p.Tyr84Cys), rs121917964, ClinGen CA284901, ClinVar RCV000059392, ClinVar RCV000255485, AlphaMissense 0.88, MetaLR 0.98, Pathogenic/Likely pathogenic, Generalized epilepsy with febrile seizures plus, type 2; Migraine, familial hemi
- I85V (p.Ile85Val), rs1574371287, ClinGen CA349242648, ClinVar RCV006464369, Ensembl rs1574371287, AlphaMissense 0.07, MetaLR 0.66, Uncertain significance, Early-infantile DEE
- N86S (p.Asn86Ser), rs1004366186, ClinGen CA60270523, cosmic curated COSV57680, ClinVar RCV002451545, CADD 24.70, PolyPhen-2 0.98, Uncertain significance, Early-infantile DEE; Inborn genetic diseases
- K87* (p.Lys87Ter), cosmic curated COSV10514, Ensembl rs1553560683
- K88* (p.Lys88Ter), Ensembl rs1553560679
- K88N (p.Lys88Asn), rs1025532519, ClinGen CA60270522, ClinVar RCV001556767, ClinVar RCV006466256, CADD 22.20, PolyPhen-2 0.00, Conflicting interpretations, not provided; Early-infantile DEE
- T89I (p.Thr89Ile), rs1574302474, ClinGen CA349077319, ClinVar RCV006265301, ClinVar RCV006464393, AlphaMissense 0.87, MetaLR 0.94, Uncertain significance, Early-infantile DEE; not specified
- F90S (p.Phe90Ser), rs121918733, ClinGen CA285078, cosmic curated COSV10961, ClinVar RCV000059473, AlphaMissense 1.00, MetaLR 0.97, Pathogenic/Likely pathogenic, Early-infantile DEE; not provided; Severe myoclonic epilepsy in infancy
- I91T (p.Ile91Thr), rs121918734, ClinGen CA285081, ClinVar RCV000059474, ClinVar RCV003157390, AlphaMissense 0.81, MetaLR 0.96, Pathogenic, Early-infantile DEE; Generalized epilepsy with febrile seizures plus, type 2; Se
- L93* (p.Leu93Ter), Ensembl rs1553553593
- N94Y (p.Asn94Tyr), rs1699367901, ClinGen CA349077255, ClinVar RCV006465223, Ensembl rs1699367901, AlphaMissense 0.93, MetaLR 0.95, Pathogenic, Early-infantile DEE
- K95* (p.Lys95Ter), Ensembl rs1553553576
- G96R (p.Gly96Arg), gnomAD rs1699367311, CADD 24.10, PolyPhen-2 1.00
- K97* (p.Lys97Ter), Ensembl rs1553553573
- A98P (p.Ala98Pro), UniProt VAR 073447, Pathogenic, in DRVT
- A98V (p.Ala98Val), rs2105918454, ClinGen CA349077190, NCI-TCGA Cosmic COSV1003, cosmic curated COSV10032, CADD 24.30, PolyPhen-2 0.93, Uncertain significance, not provided; Early-infantile DEE
- I99V (p.Ile99Val), rs2468272893, ClinGen CA349077183, ClinVar RCV006561937, NCI-TCGA TCGA novel, CADD 24.30, PolyPhen-2 0.56, Likely pathogenic, Early-infantile DEE
- F100L (p.Phe100Leu), rs2105918428, ClinGen CA349077150, ClinVar RCV006557990, Ensembl rs2105918428, AlphaMissense 0.99, MetaLR 0.92, Likely pathogenic, Early-infantile DEE
- R101L (p.Arg101Leu), rs121917918, ClinGen CA349077140, ClinVar RCV000518488, Ensembl rs121917918, AlphaMissense 0.99, MetaLR 0.97, Pathogenic, not provided
- R101Q (p.Arg101Gln), rs121917918, ClinGen CA273119, cosmic curated COSV10032, ClinVar RCV000059400, AlphaMissense 0.99, MetaLR 0.97, Pathogenic, Early-infantile DEE; Severe myoclonic epilepsy in infancy; Generalized epilepsy
- R101W (p.Arg101Trp), rs121917965, ClinGen CA284919, ClinVar RCV000059399, ClinVar RCV000357692, AlphaMissense 0.99, MetaLR 0.98, Pathogenic/Likely pathogenic, Early-infantile DEE; not provided; Migraine, familial hemiplegic, 3
- F102S (p.Phe102Ser), rs2105918357, ClinGen CA349077129, ClinVar RCV006468618, Ensembl rs2105918357, AlphaMissense 1.00, MetaLR 0.98, Pathogenic, Early-infantile DEE
- S103G (p.Ser103Gly), rs121918743, ClinGen CA285123, ClinVar RCV000059491, UniProt VAR 029662, AlphaMissense 0.52, MetaLR 0.95, not provided, Severe myoclonic epilepsy in infancy
- S103I (p.Ser103Ile), rs760361423, ClinGen CA303246, ClinVar RCV000180851, ExAC rs760361423, AlphaMissense 0.98, MetaLR 0.95, Pathogenic, Severe myoclonic epilepsy in infancy
- S103N (p.Ser103Asn), ExAC rs760361423, gnomAD rs760361423, AlphaMissense 0.98, MetaLR 0.95, Pathogenic, in DRVT
- A104D (p.Ala104Asp), rs1553553527, ClinGen CA349077094, ClinVar RCV002283507, ClinVar RCV006607697, AlphaMissense 0.92, MetaLR 0.96, Pathogenic, Early-infantile DEE; Severe myoclonic epilepsy in infancy
- A104V (p.Ala104Val), cosmic curated COSV57660, Ensembl rs1553553527, Pathogenic
- T105I (p.Thr105Ile), rs796053089, ClinGen CA317748, ClinVar RCV000189071, UniProt VAR 073448, AlphaMissense 0.21, MetaLR 0.94, Pathogenic/Likely pathogenic, not provided
- T105N (p.Thr105Asn), rs796053089, ClinGen CA59804349, ClinVar RCV002463978, ClinVar RCV004721075, AlphaMissense 0.21, MetaLR 0.94, Uncertain significance, Early-infantile DEE; not provided
- S106F (p.Ser106Phe), NCI-TCGA Cosmic COSV5765, cosmic curated COSV57658, NCI-TCGA Cosmic COSV5766, Variant assessed as somatic; moderate impact.
- S106Y (p.Ser106Tyr), NCI-TCGA Cosmic COSV5765, NCI-TCGA Cosmic COSV5766, cosmic curated COSV57664, Variant assessed as somatic; moderate impact.
- A107S (p.Ala107Ser), rs745404213, ClinGen CA1943536, ClinVar RCV006465848, ExAC rs745404213, CADD 23.50, PolyPhen-2 0.96, Uncertain significance, Early-infantile DEE
- A107V (p.Ala107Val), rs1559254819, ClinGen CA349077069, ClinVar RCV000762057, Ensembl rs1559254819, AlphaMissense 0.93, MetaLR 0.96, Uncertain significance, not provided
- L108P (p.Leu108Pro), rs794726793, ClinGen CA303399, ClinVar RCV000180910, Ensembl rs794726793, AlphaMissense 0.98, MetaLR 0.97, Pathogenic, Severe myoclonic epilepsy in infancy
- L108Q (p.Leu108Gln), rs794726793, ClinGen CA349077059, ClinVar RCV002249161, Ensembl rs794726793, AlphaMissense 0.98, MetaLR 0.97, Likely pathogenic, Generalized epilepsy with febrile seizures plus, type 2
- L108R (p.Leu108Arg), UniProt VAR 073449, Pathogenic, in DRVT
- L108V (p.Leu108Val), rs779413164, ClinGen CA1943535, ClinVar RCV006562351, ExAC rs779413164, CADD 22.80, Uncertain significance, Early-infantile DEE
- Y109* (p.Tyr109Ter), rs1553553485, ClinGen CA349077040, ClinVar RCV000504593, Ensembl rs1553553485, Pathogenic
- Y109F (p.Tyr109Phe), gnomAD rs1699359593, Uncertain significance, Early-infantile DEE
- I110V (p.Ile110Val), TOPMed rs1376528857, Uncertain significance, not provided
- T112I (p.Thr112Ile), rs121918745, ClinGen CA285126, ClinVar RCV000059492, ClinVar RCV000433130, AlphaMissense 0.76, MetaLR 0.92, Likely pathogenic, Early-infantile DEE; not provided; Severe myoclonic epilepsy in infancy
- P113L (p.Pro113Leu), rs1553553462, ClinGen CA349076987, ClinVar RCV006465207, Ensembl rs1553553462, AlphaMissense 0.98, MetaLR 0.96, Pathogenic, Early-infantile DEE
- P113R (p.Pro113Arg), rs1553553462, ClinGen CA349076981, ClinVar RCV000585829, Ensembl rs1553553462, AlphaMissense 0.98, MetaLR 0.96, Likely pathogenic, Severe myoclonic epilepsy in infancy
- P113S (p.Pro113Ser), rs794726711, ClinGen CA349076990, cosmic curated COSV57662, ClinVar RCV006468781, CADD 25.40, PolyPhen-2 0.98, Pathogenic, in DRVT
- P113T (p.Pro113Thr), rs794726711, ClinGen CA303135, ClinVar RCV000180815, ClinVar RCV000188831, CADD 25.10, PolyPhen-2 0.99, Pathogenic, Developmental and epileptic encephalopathy; not provided; Severe myoclonic epile
Public SCN1A analysis runs
- SCN1A analysis run — SCN1A (3,810 variants) — completed 2026-08-09