Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6328
Gene name Gene Name - the full gene name approved by the HGNC.	Sodium voltage-gated channel alpha subunit 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SCN3A
Synonyms (NCBI Gene) Gene synonyms aliases	DEE62, EIEE62, FFEVF4, NAC3, Nav1.3
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q24.3
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(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
rs145171998	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, 5 prime UTR variant, synonymous variant
rs145492863	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, synonymous variant
rs146624492	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, synonymous variant
rs199597878	T>A,C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs199975643	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs368608408	A>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, synonymous variant
rs370351101	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs370428859	G>A,T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic downstream transcript variant, coding sequence variant
rs371709966	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs748935500	A>T	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs755159935	A>C,G	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs755440336	C>T	Pathogenic	Missense variant, coding sequence variant
rs758906955	T>C	Pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs774195502	C>T	Uncertain-significance, pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs797044933	G>A	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant
rs1057518801	A>G	Likely-pathogenic, pathogenic-likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1057520753	G>A	Pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs1199412903	C>T	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs1553517203	AG>-	Likely-pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant
rs1553517274	A>G	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs1553537132	A>G	Likely-pathogenic	5 prime UTR variant, intron variant, coding sequence variant, missense variant
rs1574159505	CAA>-	Likely-pathogenic	Coding sequence variant, inframe deletion

Show/Hide all(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
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329961	hsa-miR-3163	CLIP-seq
MIRT1329962	hsa-miR-3613-3p	CLIP-seq
MIRT1329963	hsa-miR-4432	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT1329965	hsa-miR-4699-3p	CLIP-seq
MIRT1329966	hsa-miR-4729	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329968	hsa-miR-4803	CLIP-seq
MIRT1329969	hsa-miR-499-5p	CLIP-seq
MIRT1329970	hsa-miR-520d-5p	CLIP-seq
MIRT1329971	hsa-miR-524-5p	CLIP-seq
MIRT1329972	hsa-miR-548ac	CLIP-seq
MIRT1329973	hsa-miR-548d-3p	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT1329975	hsa-miR-548z	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329976	hsa-miR-1271	CLIP-seq
MIRT1329977	hsa-miR-132	CLIP-seq
MIRT1329978	hsa-miR-182	CLIP-seq
MIRT1329979	hsa-miR-212	CLIP-seq
MIRT1329980	hsa-miR-223	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329981	hsa-miR-3622b-5p	CLIP-seq
MIRT1329982	hsa-miR-4328	CLIP-seq
MIRT1329983	hsa-miR-4535	CLIP-seq
MIRT1329984	hsa-miR-4642	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329985	hsa-miR-492	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT1329986	hsa-miR-96	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT2097777	hsa-miR-4700-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT2097778	hsa-miR-4766-3p	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT2322068	hsa-miR-103a	CLIP-seq
MIRT2322069	hsa-miR-107	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329976	hsa-miR-1271	CLIP-seq
MIRT1329977	hsa-miR-132	CLIP-seq
MIRT1329978	hsa-miR-182	CLIP-seq
MIRT1329979	hsa-miR-212	CLIP-seq
MIRT2322070	hsa-miR-214	CLIP-seq
MIRT1329980	hsa-miR-223	CLIP-seq
MIRT2322071	hsa-miR-3121-3p	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT2322072	hsa-miR-3619-5p	CLIP-seq
MIRT1329981	hsa-miR-3622b-5p	CLIP-seq
MIRT2322073	hsa-miR-3924	CLIP-seq
MIRT2322074	hsa-miR-4279	CLIP-seq
MIRT2322075	hsa-miR-4291	CLIP-seq
MIRT1329982	hsa-miR-4328	CLIP-seq
MIRT2322076	hsa-miR-4519	CLIP-seq
MIRT1329983	hsa-miR-4535	CLIP-seq
MIRT1329984	hsa-miR-4642	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT2322077	hsa-miR-4698	CLIP-seq
MIRT2322078	hsa-miR-4728-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329985	hsa-miR-492	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT2322079	hsa-miR-628-5p	CLIP-seq
MIRT2322080	hsa-miR-761	CLIP-seq
MIRT2322081	hsa-miR-922	CLIP-seq
MIRT1329986	hsa-miR-96	CLIP-seq
MIRT1329959	hsa-miR-1183	CLIP-seq
MIRT1329976	hsa-miR-1271	CLIP-seq
MIRT1329977	hsa-miR-132	CLIP-seq
MIRT1329978	hsa-miR-182	CLIP-seq
MIRT1329979	hsa-miR-212	CLIP-seq
MIRT1329980	hsa-miR-223	CLIP-seq
MIRT1329960	hsa-miR-3137	CLIP-seq
MIRT1329981	hsa-miR-3622b-5p	CLIP-seq
MIRT1329982	hsa-miR-4328	CLIP-seq
MIRT1329983	hsa-miR-4535	CLIP-seq
MIRT1329984	hsa-miR-4642	CLIP-seq
MIRT1329964	hsa-miR-4694-3p	CLIP-seq
MIRT1329967	hsa-miR-4738-3p	CLIP-seq
MIRT1329985	hsa-miR-492	CLIP-seq
MIRT1329974	hsa-miR-548g	CLIP-seq
MIRT1329986	hsa-miR-96	CLIP-seq
MIRT2618488	hsa-miR-188-5p	CLIP-seq
MIRT2618489	hsa-miR-507	CLIP-seq
MIRT2618490	hsa-miR-557	CLIP-seq
MIRT2618488	hsa-miR-188-5p	CLIP-seq
MIRT2618489	hsa-miR-507	CLIP-seq
MIRT2618490	hsa-miR-557	CLIP-seq

Show/Hide all(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
GO:0005248	Function	Voltage-gated sodium channel activity	IBA
GO:0005248	Function	Voltage-gated sodium channel activity	IDA	35277491
GO:0005248	Function	Voltage-gated sodium channel activity	IEA
GO:0005261	Function	Monoatomic cation channel activity	IEA
GO:0005272	Function	Sodium channel activity	IEA
GO:0005886	Component	Plasma membrane	IDA	35277491
GO:0005886	Component	Plasma membrane	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0006814	Process	Sodium ion transport	NAS	9589372
GO:0009925	Component	Basal plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0016528	Component	Sarcoplasm	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034702	Component	Monoatomic ion channel complex	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IBA
GO:0048266	Process	Behavioral response to pain	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0086002	Process	Cardiac muscle cell action potential involved in contraction	IBA
GO:0086010	Process	Membrane depolarization during action potential	IDA	35277491

MIM	HGNC	e!Ensembl
182391	10590	ENSG00000153253

Protein

UniProt ID

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
AVVAMAYEEQNQATLEEAEQKEAEFQQMLEQLKKQQEEAQAVAAASAASRDFSGIGGLGE
LLESSSEASKLSSKSAKEWRNRRKKRRQREHLEGNNKGERDSFPKSESEDSVKRSSFLFS
MDGNRLTSDKKFCSPHQSLLSIRGSLFSPRRNSKTSIFSFRGRAKDVGSENDFADDEHST
FEDSESRRDSLFVPHRHGERRNSNVSQASMSSRMVPGLPANGKMHSTVDCNGVVSLVGGP
SALTSPTGQLPPEGTTTETEVRKRRLSSYQISMEMLEDSSGRQRAVSIASILTNTMEELE
ESRQKCPPCWYRFANVFLIWDCCDAWLKVKHLVNLIVMDPFVDLAITICIVLNTLFMAME
HYPMTEQFSSVLTVGNLVFTGIFTAEMVLKIIAMDPYYYFQEGWNIFDGIIVSLSLMELG
LSNVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVG
MQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMC
LIVFMLVMVIGNLVVLNLFLALLLSSFSSDNLAATDDDNEMNNLQIAVGRMQKGIDYVKN
KMRECFQKAFFRKPKVIEIHEGNKIDSCMSNNTGIEISKELNYLRDGNGTTSGVGTGSSV
EKYVIDENDYMSFINNPSLTVTVPIAVGESDFENLNTEEFSSESELEESKEKLNATSSSE
GSTVDVVLPREGEQAETEPEEDLKPEACFTEGCIKKFPFCQVSTEEGKGKIWWNLRKTCY
SIVEHNWFETFIVFMILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTYIFILEMLLKWV
AYGFQTYFTNAWCWLDFLIVDVSLVSLVANALGYSELGAIKSLRTLRALRPLRALSRFEG
MRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFYHCVNMTTGNMFDISDVNN
LSDCQALGKQARWKNVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRDVKLQPVYEE
NLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLG
SKKPQKPIPRPANKFQGMVFDFVTRQVFDISIMILICLNMVTMMVETDDQGKYMTLVLSR
INLVFIVLFTGEFVLKLVSLRHYYFTIGWNIFDFVVVILSIVGMFLAEMIEKYFVSPTLF
RVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYV
KKEAGIDDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSAPPDCDPDTIHPGSSVKGD
CGNPSVGIFFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYEVWEKF
DPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRV
LGESGEMDALRIQMEDRFMASNPSKVSYEPITTTLKRKQEEVSAAIIQRNFRCYLLKQRL
KNISSNYNKEAIKGRIDLPIKQDMIIDKLNGNSTPEKTDGSSSTTSPPSYDSVTKPDKEK
FEKDKPEKESKGKEVRENQK

Sequence length

2000

Interactions

View interactions

	KEGG		Reactome
	Taste transduction		Phase 0 - rapid depolarisation

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Developmental And Epileptic Encephalopathy	Developmental and epileptic encephalopathy, 62	rs1057518801, rs1574159505, rs755159935, rs1057520753, rs1553537132, rs1199412903, rs1553517274	N/A
Epilepsy	epilepsy, familial focal, with variable foci 4, epilepsy	rs2105890565, rs1057518801	N/A
Epileptic Encephalopathy	early infantile epileptic encephalopathy with suppression bursts	rs1057518801, rs755159935, rs1689488709, rs1057520753, rs1199412903, rs1553517274	N/A

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
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
Epileptic Encephalopathy Early Infantile 3	Associate	36571524
Frasier Syndrome	Associate	33895391
Generalized Epilepsy With Febrile Seizures Plus Type 1	Associate	10486327
Heart Diseases	Associate	30212560
Intellectual Disability	Associate	32515017
Malformations of Cortical Development	Associate	32515017, 37935051
Nerve Degeneration	Associate	24157691
Pain	Associate	37531097
Polymicrogyria	Associate	29466837, 37486637
REM Sleep Behavior Disorder	Associate	32986685
Seizures	Associate	10486327, 30071822
Seizures Febrile	Associate	10486327
Spasms Infantile	Associate	29929112
Sudden Infant Death	Associate	37995443
Synucleinopathies	Associate	32986685
Tetralogy of Fallot	Associate	30212560
Tourette Syndrome	Associate	30071822

SCN3A (sodium voltage-gated channel alpha subunit 3)