Gene info: ID 6328

Gene: SCN3A

GENE ID: 6328

Synonyms: EIEE62|FFEVF4|NAC3|Nav1.3

Description: sodium voltage-gated channel alpha subunit 3

Gene type: protein-coding

Location: 2q24.3

dbXrefs: Ensembl:ENSG00000153253 MIM:182391 Vega:OTTHUMG00000044171 UniprotKB:Q9NY46

RefSeq: NG_042289.1

Retrived from: SNP Mapped

SNPs: 2 ANCO-SNPs

Phenotype: AD

# Publications: 0

Sherlock p-value : NA (AD) NA (ND) (Frontal_Cortex)

Pascal p-value : 5.952e-1 (AD) 1.195e-1 (ND)

ANCO-SNPs

SNP ID	Position	Alleles	Trait	Variation Type
rs1347992	chr2:165105355 (GRCh38.p7)	T>C	alcohol dependence	SNV(Single Nucleotide Variation)
rs3816195	chr2:165099998 (GRCh38.p7)	T>G	alcohol dependence	SNV(Single Nucleotide Variation)

DNA Methylation

There is no related methylation information for this gene.

Gene Expression in Different Tissues

Temporal and Spatial Expressions (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes average value of the expressions.

Top Co-expressed Genes in Brain-Frontal Cortex (BA9) (GTEx v7)

Top 10 positively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
RGS17	0.89
ZDBF2	0.881
FAM117B	0.873
CSMD3	0.872
ARL14EP	0.869
RNF2	0.866
ABHD13	0.866
PGAP1	0.865
CSNK1G3	0.864
KIAA0895	0.86

Top 10 negatively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
OR4F5	-0.411
CSAG1	-0.393
COPZ2	-0.37
OR4F29	-0.364
S100A14	-0.363
SOD3	-0.362
ASB4	-0.361
RHOD	-0.36
CYP11A1	-0.355
TBX2	-0.352

ID	Drug Name	Drug Type	CAS Num	Status	Role
DB00252	Phenytoin	Small Molecule	57-41-0	Approved	Target
DB00909	Zonisamide	Small Molecule	68291-97-4	Approved\|Investigational	Target
DB05232	Tetrodotoxin	Small Molecule	4368-28-9	Investigational	Target
DB06218	Lacosamide	Small Molecule	175481-36-4	Approved	Target
DB00313	Valproic Acid	Small Molecule	99-66-1	Approved\|Investigational	Target
DB05541	Brivaracetam	Small Molecule	357336-20-0	Approved\|Investigational	Target

ID	Drug Name	Action	PubMed
C006718	1,12-benzoperylene	"1,12-benzoperylene results in increased expression of SCN3A mRNA"	26377693
C070379	1,2-bis(2-aminophenoxy)ethane N,N,N',N'-tetraacetic acid acetoxymethyl ester	"1,2-bis(2-aminophenoxy)ethane N,N,N',N'-tetraacetic acid acetoxymethyl ester inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]"	25358543
C511295	2,2',4,4'-tetrabromodiphenyl ether	"2,2',4,4'-tetrabromodiphenyl ether results in decreased expression of SCN3A mRNA"	27291303
C111118	2',3,3',4',5-pentachloro-4-hydroxybiphenyl	"2',3,3',4',5-pentachloro-4-hydroxybiphenyl results in decreased expression of SCN3A mRNA"	19114083
C489827	2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylate	"2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylate inhibits the reaction [[SCN3A protein co-treated with SCN2B protein co-treated with SCN1B protein] results in increased transport of Sodium]"	19026681
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with vorinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with vorinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386
C014949	acetylhydrazine	acetylhydrazine results in decreased expression of SCN3A mRNA	15282401
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of SCN3A mRNA	16483693
D018501	Antirheumatic Agents	Antirheumatic Agents results in decreased expression of SCN3A mRNA	24449571
C475726	APETx1, Anthopleura elegantissima	"APETx1, Anthopleura elegantissima analog results in decreased activity of SCN3A protein"	22972919
C475726	APETx1, Anthopleura elegantissima	"APETx1, Anthopleura elegantissima results in decreased activity of SCN3A protein"	22972919
D001151	Arsenic	Arsenic results in decreased expression of SCN3A mRNA	19654921
D015123	7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	"7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide results in increased expression of SCN3A mRNA"	20382639
C006780	bisphenol A	bisphenol A results in increased expression of SCN3A mRNA	29275510
C006780	bisphenol A	bisphenol A results in decreased expression of SCN3A mRNA	25181051
D002104	Cadmium	Cadmium results in decreased expression of SCN3A mRNA	21120746
D002737	Chloroprene	Chloroprene results in decreased expression of SCN3A mRNA	23125180
C052570	cyfluthrin	cyfluthrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
C017160	cypermethrin	cypermethrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
C010902	decabromobiphenyl ether	decabromobiphenyl ether results in decreased expression of SCN3A mRNA	23640034
C017180	decamethrin	"1,2-bis(2-aminophenoxy)ethane N,N,N',N'-tetraacetic acid acetoxymethyl ester inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]"	25358543
C017180	decamethrin	decamethrin results in decreased expression of SCN3A mRNA	25358543
C017180	decamethrin	PD 150606 inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]	25358543
C017180	decamethrin	Tetrodotoxin inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]	25358543
C017180	decamethrin	decamethrin results in decreased expression of SCN3A mRNA	27058123
D004997	Ethinyl Estradiol	Ethinyl Estradiol results in decreased expression of SCN3A mRNA	15834898
C044267	fenpropathrin	fenpropathrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
C017690	fenvalerate	fenvalerate affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
D005419	Flavonoids	Flavonoids results in increased expression of SCN3A mRNA	18035473
D005492	Folic Acid	Folic Acid results in increased expression of SCN3A mRNA	25006883
C039281	furan	furan results in decreased methylation of SCN3A gene	22079235
D007545	Isoproterenol	Isoproterenol results in increased expression of SCN3A mRNA	20003209
C004925	methylmercuric chloride	methylmercuric chloride results in decreased expression of SCN3A mRNA	23103053
D015655	1-Methyl-4-phenylpyridinium	1-Methyl-4-phenylpyridinium results in decreased expression of SCN3A mRNA	24810058
C500085	muraglitazar	muraglitazar results in decreased expression of SCN3A mRNA	21515302
C561228	N-(2-methyl-3-(4-(4-(4-(trifluoromethoxy)benzyloxy)piperidin-1-yl)-1,3,5-triazin-2-ylamino)phenyl)acetamide	"N-(2-methyl-3-(4-(4-(4-(trifluoromethoxy)benzyloxy)piperidin-1-yl)-1,3,5-triazin-2-ylamino)phenyl)acetamide results in decreased activity of SCN3A protein"	21634377
D037742	Nanotubes, Carbon	"Nanotubes, Carbon analog results in decreased expression of SCN3A mRNA"	25554681
D037742	Nanotubes, Carbon	"Nanotubes, Carbon results in decreased expression of SCN3A mRNA"	25554681
D009532	Nickel	Nickel results in decreased expression of SCN3A mRNA	25583101
C100442	PD 150606	PD 150606 inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]	25358543
D010672	Phenytoin	Phenytoin binds to [SCN1B protein binds to SCN3A protein]	15922564
D010672	Phenytoin	Phenytoin results in decreased activity of [SCN1B protein binds to SCN3A protein]	15922564
C006253	pirinixic acid	pirinixic acid results in decreased expression of SCN3A mRNA	19162173
D011192	Potassium Dichromate	Potassium Dichromate results in decreased expression of SCN3A mRNA	23608068
D011441	Propylthiouracil	Propylthiouracil results in increased expression of SCN3A mRNA	24780913
C089730	rosiglitazone	rosiglitazone results in decreased expression of SCN3A mRNA	21515302
D012604	Scorpion Venoms	Scorpion Venoms affects the activity of SCN3A protein	21887265
D012834	Silver	Silver results in decreased expression of SCN3A mRNA	27131904
D012964	Sodium	"2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylate inhibits the reaction [[SCN3A protein co-treated with SCN2B protein co-treated with SCN1B protein] results in increased transport of Sodium]"	19026681
D012964	Sodium	[SCN3A protein co-treated with SCN2B protein co-treated with SCN1B protein] results in increased transport of Sodium	19026681
D012964	Sodium	cyfluthrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
D012964	Sodium	cypermethrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
D012964	Sodium	fenpropathrin affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
D012964	Sodium	fenvalerate affects the reaction [[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium]	18538810
D012964	Sodium	[SCN3A protein binds to SCN3B protein] which results in increased transport of Sodium	18538810
D053260	Soot	Soot results in decreased expression of SCN3A mRNA	26551751
D013779	Tetrodotoxin	Tetrodotoxin inhibits the reaction [decamethrin results in decreased expression of SCN3A mRNA]	25358543
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution affects the expression of SCN3A mRNA	20133372
C012589	trichostatin A	trichostatin A results in increased expression of SCN3A mRNA	24935251\|2670570
C057693	troglitazone	troglitazone results in decreased expression of SCN3A mRNA	21515302
C022884	undecane	undecane results in increased expression of SCN3A protein	17337753
D014635	Valproic Acid	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386
D014635	Valproic Acid	Valproic Acid affects the expression of SCN3A mRNA	25979313
D014635	Valproic Acid	Valproic Acid results in decreased methylation of SCN3A gene	29154799
D014635	Valproic Acid	Valproic Acid results in increased expression of SCN3A mRNA	23179753\|2438349
D001335	Vehicle Emissions	Vehicle Emissions results in decreased methylation of SCN3A gene	25560391
C111237	vorinostat	"[NOG protein co-treated with vorinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of SCN3A mRNA"	27188386

GO/Pathway

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0005244	voltage-gated ion channel activity	-	IEA	-
GO:0005248	voltage-gated sodium channel activity	-	IBA	21873635
GO:0005248	voltage-gated sodium channel activity	-	NAS	9589372
GO:0005261	cation channel activity	-	IBA	21873635

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0006814	sodium ion transport	-	NAS	9589372
GO:0019228	neuronal action potential	-	IBA	21873635
GO:0034765	regulation of ion transmembrane transport	-	IEA	-
GO:0035725	sodium ion transmembrane transport	-	IBA	21873635
GO:0035725	sodium ion transmembrane transport	-	IEA	-
GO:0086010	membrane depolarization during action potential	-	IBA	21873635

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0001518	voltage-gated sodium channel complex	-	IEA	-
GO:0005737	cytoplasm	-	IEA	-
GO:0005886	plasma membrane	-	IBA	21873635

KEGG ID	KEGG Term

Reactome ID	Reactome Term	Evidence
R-HSA-1266738	Developmental Biology	IEA
R-HSA-373760	L1CAM interactions	IEA
R-HSA-397014	Muscle contraction	TAS
R-HSA-422475	Axon guidance	IEA
R-HSA-445095	Interaction between L1 and Ankyrins	IEA
R-HSA-5576891	Cardiac conduction	TAS
R-HSA-5576892	Phase 0 - rapid depolarisation	TAS

Interactions (STRING v10.5, Interaction Score >= 0.400)

Publications (Co-occurrence of gene symbol strings and ANCO-Dependence terms)

PMID	Title (Year)	Author	Journal