Gene Gene information from NCBI Gene database.
Entrez ID 6328
Gene name Sodium voltage-gated channel alpha subunit 3
Gene symbol SCN3A
Synonyms (NCBI Gene)
DEE62EIEE62FFEVF4NAC3Nav1.3
Chromosome 2
Chromosome location 2q24.3
Summary Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials i
SNPs SNP information provided by dbSNP.
27
SNP ID Visualize variation Clinical significance Consequence
rs76144052 A>G Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant, missense variant
rs138331141 T>C Conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs138766015 A>G Conflicting-interpretations-of-pathogenicity Genic downstream transcript variant, coding sequence variant, synonymous variant
rs139769668 C>A,T Conflicting-interpretations-of-pathogenicity 5 prime UTR variant, coding sequence variant, missense variant
rs143360102 G>C Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
miRNA miRNA information provided by mirtarbase database.
106
miRTarBase ID miRNA Experiments Reference
MIRT018072 hsa-miR-335-5p Microarray 18185580
MIRT022759 hsa-miR-124-3p Microarray 18668037
MIRT023856 hsa-miR-1-3p Microarray 18668037
MIRT1329958 hsa-miR-1179 CLIP-seq
MIRT1329959 hsa-miR-1183 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
25
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 IDA 35277491
GO:0001518 Component Voltage-gated sodium channel complex IEA
GO:0005216 Function Monoatomic ion channel activity IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
182391 10590 ENSG00000153253
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NY46
Protein name Sodium channel protein type 3 subunit alpha (Sodium channel protein brain III subunit alpha) (Sodium channel protein type III subunit alpha) (Voltage-gated sodium channel subtype III) (Voltage-gated sodium channel subunit alpha Nav1.3)
Protein function Pore-forming subunit of Nav1.3, 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 7W77 , 7W7F
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00520 Ion_trans 127 435 Ion transport protein Family
PF11933 Na_trans_cytopl 507 710 Cytoplasmic domain of voltage-gated Na+ ion channel Family
PF00520 Ion_trans 759 994 Ion transport protein Family
PF06512 Na_trans_assoc 998 1201 Sodium ion transport-associated Family
PF00520 Ion_trans 1205 1478 Ion transport protein Family
PF00520 Ion_trans 1525 1782 Ion transport protein Family
Tissue specificity TISSUE SPECIFICITY: Expressed in enterochromaffin cells in both colon and small bowel (at protein level). {ECO:0000269|PubMed:29142310}.
Sequence
MAQALLVPPGPESFRLFTRESLAAIEKRAAEEKAKKPKKEQDNDDENKPKPNSDLEAGKN
LPFIYGDIPPEMVSEPLEDLDPYYINKKTFIVMNKGKAIFRFSATSALYILTPLNPVRKI
AIKILVHSLFSMLIMCTILTNCVFMTLSNPPDWTKNVEYTFTGIYTFESLIKILARGFCL
EDFTFLRDPWNWLDFSVIVMAYVTEFVSLGNVSALRTFRVLRALKTISVIPGLKTIVGAL
IQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLRNKCLQWPPSDSAFETNTTSYFNGTMD
SNGTFVNVTMSTFNWKDYIGDDSHFYVLDGQKDPLLCGNGSDAGQCPEGYICVKAGRNPN
YGYTSFDTFSWAFLSLFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFLGSFYLVNLIL
AVVAMAYEEQNQATL
EEAEQKEAEFQQMLEQLKKQQEEAQAVAAASAASRDFSGIGGLGE
LLESSSEASKLSSKSAKEWRNRRKKRRQREHLEGNNKGERDSFPKSESEDSVKRSSFLFS
MDGNRLTSDKKFCSPHQSLLSIRGSLFSPRRNSKTSIFSFRGRAKDVGSENDFADDEHST
FEDSESRRDSLFVPHRHGERRNSNVSQASMSSRMVPGLPANGKMHSTVDCNGVVSLVGGP
SALTSPTGQLPPEGTTTETEVRKRRLSSYQISMEMLEDSSGRQRAVSIAS
ILTNTMEELE
ESRQKCPPCWYRFANVFLIWDCCDAWLKVKHLVNLIVMDPFVDLAITICIVLNTLFMAME
HYPMTEQFSSVLTVGNLVFTGIFTAEMVLKIIAMDPYYYFQEGWNIFDGIIVSLSLMELG
LSNVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVG
MQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMC
LIVFMLVMVIGNLVVLNLFLALLLSSFSSDNLAA
TDDDNEMNNLQIAVGRMQKGIDYVKN
KMRECFQKAFFRKPKVIEIHEGNKIDSCMSNNTGIEISKELNYLRDGNGTTSGVGTGSSV
EKYVIDENDYMSFINNPSLTVTVPIAVGESDFENLNTEEFSSESELEESKEKLNATSSSE
GSTVDVVLPREGEQAETEPEEDLKPEACFTEGCIKKFPFCQVSTEEGKGKIWWNLRKTCY
S
IVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTYIFILEMLLKWV
AYGFQTYFTNAWCWLDFLIVDVSLVSLVANALGYSELGAIKSLRTLRALRPLRALSRFEG
MRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYHCVNMTTGNMFDISDVNN
LSDCQALGKQARWKNVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRDVKLQPVYEE
NLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKF
GGQDIFMTEEQKKYYNAMKKLG
SKKPQKPIPRPANKFQGMVFDFVTRQVFDISIMILICLNMVTMMVETDDQGKYMTLVLSR
INLVFIVLFTGEFVLKLVSLRHYYFTIGWNIFDFVVVILSIVGMFLAEMIEKYFVSPTLF
RVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYV
KKEAGIDDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSAPPDCDPDTIHPGSSVKGD
CGNPSVGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESA
EPLSEDDFEMFYEVWEKF
DPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRV
LGESGEMDALRIQMEDRFMASNPSKVSYEPITTTLKRKQEEVSAAIIQRNFRCYLLKQRL
KNISSNYNKEAIKGRIDLPIKQDMIIDKLNGNSTPEKTDGSSSTTSPPSYDSVTKPDKEK
FEKDKPEKESKGKEVRENQK
Sequence length 2000
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Taste transduction   Phase 0 - rapid depolarisation
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
255
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
atypical cerebral palsy Likely pathogenic rs1553537132 RCV000655959
Congenital bilateral perisylvian syndrome Likely pathogenic; Pathogenic rs1199412903 RCV003446092
Developmental and epileptic encephalopathy Likely pathogenic; Pathogenic rs2105776898, rs2105636234, rs2105621335, rs2105895111, rs1057518801, rs1057520753, rs1199412903, rs1553517274, rs755159935, rs1689488709 RCV003992557
RCV003992558
RCV003992559
RCV004577557
RCV003243119
RCV003992291
RCV003992303
RCV003992349
RCV003992431
RCV003992444
Developmental and epileptic encephalopathy, 62 Likely pathogenic; Pathogenic rs1685039783, rs2105776898, rs2105772689, rs2105636234, rs2105635851, rs2105621618, rs2105621335, rs2105619771, rs1553527930, rs1574270768, rs1057518801, rs1057520753, rs1553537132, rs1199412903, rs1553517274
View all (2 more)
RCV001775229
RCV001800240
RCV001800241
RCV001800242
RCV001800243
RCV001800244
RCV001800245
RCV001800246
RCV002465081
RCV003988169
RCV000625712
RCV000625713
RCV002250643
RCV001799670
RCV000625714
RCV000986847
RCV001799715
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Developmental and epileptic encephalopathy, 1 Uncertain significance rs150421779 RCV005429075
Epilepsy, familial focal, with variable foci 1 Uncertain significance rs774354894 RCV003339757
Epilepsy, focal, SCN3A related Uncertain significance rs1259701704, rs530839611 RCV005863262
RCV001824891
Epilepsy, idiopathic generalized, susceptibility to, 7 Uncertain significance rs2105834282 RCV001808936
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Autism Spectrum Disorder Associate 29929112, 30071822
Brain Diseases Associate 29466837, 37935051
Central Nervous System Vascular Malformations Associate 32515017
Channelopathies Associate 32515017
Death Sudden Associate 37995443
Depressive Disorder Treatment Resistant Associate 32515017
Developmental Disabilities Associate 32515017
Epilepsies Partial Associate 18242854, 24157691
Epilepsy Associate 18242854, 21893419, 24157691, 28074849, 32515017, 35801810, 37995443
Epilepsy Benign Neonatal Associate 21893419