Gene Gene information from NCBI Gene database.
Entrez ID 6323
Gene name Sodium voltage-gated channel alpha subunit 1
Gene symbol SCN1A
Synonyms (NCBI Gene)
DEE6DEE6ADEE6BDRVTEIEE6FEB3FEB3AFHM3GEFSP2HBSCINAC1Nav1.1SCN1SMEI
Chromosome 2
Chromosome location 2q24.3
Summary Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium cha
SNPs SNP information provided by dbSNP.
396
SNP ID Visualize variation Clinical significance Consequence
rs3812718 C>T Drug-response, risk-factor Intron variant
rs35595680 G>-,GG Pathogenic Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant
rs114137271 T>C,G Conflicting-interpretations-of-pathogenicity, benign, likely-benign Non coding transcript variant, 5 prime UTR variant, synonymous variant, coding sequence variant
rs116478064 G>A Benign, conflicting-interpretations-of-pathogenicity Non coding transcript variant, 5 prime UTR variant, synonymous variant, coding sequence variant
rs121917918 C>A,T Pathogenic Non coding transcript variant, 5 prime UTR variant, coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
163
miRTarBase ID miRNA Experiments Reference
MIRT038738 hsa-miR-93-3p CLASH 23622248
MIRT613603 hsa-miR-548c-3p HITS-CLIP 23824327
MIRT613601 hsa-miR-4668-3p HITS-CLIP 23824327
MIRT613600 hsa-miR-3127-3p HITS-CLIP 23824327
MIRT613599 hsa-miR-6756-3p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
53
GO ID Ontology Definition Evidence Reference
GO:0001508 Process Action potential IEA
GO:0001518 Component Voltage-gated sodium channel complex IBA
GO:0001518 Component Voltage-gated sodium channel complex IEA
GO:0005216 Function Monoatomic ion channel activity IEA
GO:0005248 Function Voltage-gated sodium channel activity IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
182389 10585 ENSG00000144285
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P35498
Protein name Sodium channel protein type 1 subunit alpha (Sodium channel protein brain I subunit alpha) (Sodium channel protein type I subunit alpha) (Voltage-gated sodium channel subunit alpha Nav1.1)
Protein function Pore-forming subunit of Nav1.1, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes. Navs, also called VGSCs (voltage-gated sodium channels) or VDSCs (voltage-dependent s
PDB 7DTD
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00520 Ion_trans 127 434 Ion transport protein Family
PF11933 Na_trans_cytopl 501 718 Cytoplasmic domain of voltage-gated Na+ ion channel Family
PF00520 Ion_trans 767 1002 Ion transport protein Family
PF06512 Na_trans_assoc 1006 1213 Sodium ion transport-associated Family
PF00520 Ion_trans 1217 1493 Ion transport protein Family
PF00520 Ion_trans 1540 1797 Ion transport protein Family
Sequence
MEQTVLVPPGPDSFNFFTRESLAAIERRIAEEKAKNPKPDKKDDDENGPKPNSDLEAGKN
LPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVLNKGKAIFRFSATSALYILTPFNPLRKI
AIKILVHSLFSMLIMCTILTNCVFMTMSNPPDWTKNVEYTFTGIYTFESLIKIIARGFCL
EDFTFLRDPWNWLDFTVITFAYVTEFVDLGNVSALRTFRVLRALKTISVIPGLKTIVGAL
IQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLRNKCIQWPPTNASLEEHSIEKNITVNY
NGTLINETVFEFDWKSYIQDSRYHYFLEGFLDALLCGNSSDAGQCPEGYMCVKAGRNPNY
GYTSFDTFSWAFLSLFRLMTQDFWENLYQLTLRAAGKTYMIFFVLVIFLGSFYLINLILA
VVAMAYEEQNQATL
EEAEQKEAEFQQMIEQLKKQQEAAQQAATATASEHSREPSAAGRLS
DSSSEASKLSSKSAKERRNRRKKRKQKEQSGGEEKDEDEFQKSESEDSIRRKGFRFSIEG
NRLTYEKRYSSPHQSLLSIRGSLFSPRRNSRTSLFSFRGRAKDVGSENDFADDEHSTFED
NESRRDSLFVPRRHGERRNSNLSQTSRSSRMLAVFPANGKMHSTVDCNGVVSLVGGPSVP
TSPVGQLLPEVIIDKPATDDNGTTTETEMRKRRSSSFHVSMDFLEDPSQRQRAMSIAS
IL
TNTVEELEESRQKCPPCWYKFSNIFLIWDCSPYWLKVKHVVNLVVMDPFVDLAITICIVL
NTLFMAMEHYPMTDHFNNVLTVGNLVFTGIFTAEMFLKIIAMDPYYYFQEGWNIFDGFIV
TLSLVELGLANVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAII
VFIFAVVGMQLFGKSYKDCVCKIASDCQLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCM
EVAGQAMCLTVFMMVMVIGNLVVLNLFLALLLSSFSADNLAA
TDDDNEMNNLQIAVDRMH
KGVAYVKRKIYEFIQQSFIRKQKILDEIKPLDDLNNKKDSCMSNHTAEIGKDLDYLKDVN
GTTSGIGTGSSVEKYIIDESDYMSFINNPSLTVTVPIAVGESDFENLNTEDFSSESDLEE
SKEKLNESSSSSEGSTVDIGAPVEEQPVVEPEETLEPEACFTEGCVQRFKCCQINVEEGR
GKQWWNLRRTCFR
IVEHNWFETFIVFMILLSSGALAFEDIYIDQRKTIKTMLEYADKVFT
YIFILEMLLKWVAYGYQTYFTNAWCWLDFLIVDVSLVSLTANALGYSELGAIKSLRTLRA
LRPLRALSRFEGMRVVVNALLGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYHCINTT
TGDRFDIEDVNNHTDCLKLIERNETARWKNVKVNFDNVGFGYLSLLQVATFKGWMDIMYA
AVDSRNVELQPKYEESLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKF
GGQDIFM
TEEQKKYYNAMKKLGSKKPQKPIPRPGNKFQGMVFDFVTRQVFDISIMILICLNMVTMMV
ETDDQSEYVTTILSRINLVFIVLFTGECVLKLISLRHYYFTIGWNIFDFVVVILSIVGMF
LAELIEKYFVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLV
MFIYAIFGMSNFAYVKREVGIDDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSKPPD
CDPNKVNPGSSVKGDCGNPSVGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESA
EPL
SEDDFEMFYEVWEKFDPDATQFMEFEKLSQFAAALEPPLNLPQPNKLQLIAMDLPMVSGD
RIHCLDILFAFTKRVLGESGEMDALRIQMEERFMASNPSKVSYQPITTTLKRKQEEVSAV
IIQRAYRRHLLKRTVKQASFTYNKNKIKGGANLLIKEDMIIDRINENSITEKTDLTMSTA
ACPPSYDRVTKPIVEKHEQEGKDEKAKGK
Sequence length 2009
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Dopaminergic synapse   Phase 0 - rapid depolarisation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
93
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Autism Pathogenic; Likely pathogenic rs794726827, rs121917994 RCV001003957
RCV001003955
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal dominant epilepsy Likely pathogenic; Pathogenic rs2105862149, rs794726730, rs797045940, rs794726762, rs121918622, rs2468221702, rs1553520268, rs2468200195, rs751533302, rs1553546836, rs77216276, rs1559118914, rs121917993, rs121917935, rs1689682880
View all (1 more)
RCV002271866
RCV001824659
RCV001192960
RCV002469061
RCV001192959
View all (11 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Developmental and epileptic encephalopathy Likely pathogenic; Pathogenic rs121918792, rs1689381070, rs1689707865, rs1553531134, rs1698198046, rs794726749, rs779184118, rs796053040, rs528239871, rs760906812, rs2105429381, rs2105432780, rs2105610047, rs794726725, rs746413385
View all (955 more)
RCV001325213
RCV001312722
RCV001327294
RCV001325214
RCV001323407
View all (1072 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Developmental and epileptic encephalopathy 6B Likely pathogenic; Pathogenic rs746413385, rs886042528, rs1696624989, rs1553549667, rs2105486615, rs2105889878, rs2105901693, rs2105861548, rs2105433731, rs2105806338, rs1553520107, rs727504136, rs794726739, rs794726726, rs199727342
View all (43 more)
RCV004546642
RCV001420525
RCV005429056
RCV005023255
RCV004796692
View all (53 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute encephalopathy Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHROGRYPOSIS Disgenet
Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute encephalopathy Encephalopathy BEFREE 20491869, 22309220, 23034800, 23808377
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Acute encephalopathy with biphasic seizures and late reduced diffusion Encephalopathy With Biphasic Seizures And Diffusion BEFREE 22309220, 25156649, 26311622
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 18347169, 20869761, 21889186
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 38061235 Associate
★☆☆☆☆
Found in Text Mining only
Angelman Syndrome Angelman syndrome Pubtator 36750385 Associate
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety Disorder BEFREE 19464195
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety disorder Pubtator 19464195 Associate
★☆☆☆☆
Found in Text Mining only
Apnea Apnea Pubtator 35696452 Associate
★☆☆☆☆
Found in Text Mining only
Arrhythmias Cardiac Cardiac arrhythmias Pubtator 30146492 Associate
★☆☆☆☆
Found in Text Mining only