AutismKB 2.0

Annotation Detail for SCN9A


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Basic Information Top
Gene Symbol:SCN9A ( ETHA,FEB3B,NE-NA,NENA,Nav1.7,PN1 )
Gene Full Name: sodium channel, voltage-gated, type IX, alpha subunit
Band: 2q24.3
Quick LinksEntrez ID:6335; OMIM: 603415; Uniprot ID:SCN9A_HUMAN; ENSEMBL ID: ENSG00000169432; HGNC ID: 10597
Relate to Another Database: SFARIGene; denovo-db
Related Pathway Information Top
Related Diseases/Disorders Top
No data
Desease IDDesease Name
1806Arteriopathy
1831Prostate cancer
No data
No data
Desease Name
Insensitivity to pain, channelopathy-associated
Erythermalgia, primary
Paroxysmal extreme pain disorder
Febrile convulsions, familial, 3B
Comparative Toxicogenomics Database Top
Chemical ID Chemical Name Interaction Interaction Action Publication
D000643 Ammonium Chloride Ammonium Chloride affects the expression of SCN9A mRNAaffects expression 16483693
D001564 Benzo(a)pyrene Benzo(a)pyrene results in decreased expression of SCN9A mRNAdecreases expression 20106945
C546612 brevetoxin 3 brevetoxin 3 binds to SCN9A proteinaffects binding 19486905
D002118 Calcium [Lithium Chloride results in increased expression of SCN9A protein] which results in increased uptake of Calciumincreases expression|increases uptake 19486905
D002220 Carbamazepine SCN9A gene mutant form affects the susceptibility to Carbamazepineaffects response to substance 17145499
D002395 Catecholamines [Lithium Chloride results in increased expression of SCN9A protein] which results in increased secretion of Catecholaminesincreases expression|increases secretion 19486905
D000431 Ethanol [Fish Oils co-treated with Ethanol] results in increased expression of SCN9A mRNAaffects cotreatment|increases expression 17347304
D005395 Fish Oils [Fish Oils co-treated with Ethanol] results in increased expression of SCN9A mRNAaffects cotreatment|increases expression 17347304
D018021 Lithium Chloride [Lithium Chloride results in decreased activity of GSK3B protein] which results in increased expression of SCN9A mRNAdecreases activity|increases expression 19486905
D018021 Lithium Chloride Lithium Chloride results in increased expression of SCN9A mRNAincreases expression 19486905
D018021 Lithium Chloride Lithium Chloride results in increased expression of SCN9A proteinincreases expression 19486905
D018021 Lithium Chloride [Lithium Chloride results in increased expression of SCN9A protein] which results in increased secretion of Catecholaminesincreases expression|increases secretion 19486905
D018021 Lithium Chloride [Lithium Chloride results in increased expression of SCN9A protein] which results in increased uptake of Calciumincreases expression|increases uptake 19486905
D018021 Lithium Chloride [Lithium Chloride results in increased expression of SCN9A protein] which results in increased uptake of Sodiumincreases expression|increases uptake 19486905
D012530 Saxitoxin Saxitoxin binds to SCN9A proteinaffects binding 19486905
D012643 Selenium Selenium results in increased expression of SCN9A mRNAincreases expression 18583539
D012964 Sodium [Lithium Chloride results in increased expression of SCN9A protein] which results in increased uptake of Sodiumincreases expression|increases uptake 19486905
D012964 Sodium SCN9A protein results in increased transport of Sodiumincreases transport 16020462
D012964 Sodium Tetrodotoxin inhibits the reaction [SCN9A protein results in increased transport of Sodium]decreases reaction|increases transport 16020462
D013749 Tetrachlorodibenzodioxin Tetrachlorodibenzodioxin results in decreased expression of SCN9A mRNAdecreases expression 20106945
D013779 Tetrodotoxin Tetrodotoxin inhibits the reaction [SCN9A protein results in increased transport of Sodium]decreases reaction|increases transport 16020462
D014635 Valproic Acid Valproic Acid results in increased expression of SCN9A mRNAincreases expression 19101580
Disease ID Disease Name Direct Evidence Inference Chemical Name Inference Score Publication
MESH:D000014 Abnormalities, Drug-Induced Carbamazepine 20.878986270
MESH:D000014 Abnormalities, Drug-Induced Ethanol 20.8718926900 17676605
MESH:D000014 Abnormalities, Drug-Induced Tetrachlorodibenzodioxin 20.8711752688 15322242 14514962
MESH:D000014 Abnormalities, Drug-Induced Valproic Acid 20.878875741
MESH:D000015 Abnormalities, Multiple Valproic Acid 3.9619490988
MESH:D000138 Acidosis Ammonium Chloride 10.6418287403
MESH:D000138 Acidosis Ethanol 10.6411192467
MESH:D000230 Adenocarcinoma Benzo(a)pyrene 1.9920127859 20464547
MESH:D000236 Adenoma Benzo(a)pyrene 2.676695378
MESH:D018248 Adenoma, Liver Cell Tetrachlorodibenzodioxin 3.4316835633
MESH:D000303 Adrenal Cortex Diseases Catecholamines 7.386895166
MESH:D020268 Alcohol-Induced Disorders, Nervous System Ethanol 5.3815451040 15451039
MESH:D000550 Amblyopia Valproic Acid 5.3017688650
MESH:D000740 Anemia Tetrachlorodibenzodioxin 2.9711748828
MESH:D000853 Anophthalmos Ethanol 4.8615513904
MESH:D001008 Anxiety Disorders Ethanol 9.0611141031
MESH:D001008 Anxiety Disorders Valproic Acid 9.0617497229
MESH:D017544 Aortic Aneurysm, Abdominal Benzo(a)pyrene 4.1219183758
MESH:D001321 Autistic Disorder Valproic Acid 2.0015238991 17507914 20603192 17688650 18985861 18316065 18940202 18177632 19460635 18558336 19232924 18396377 17157402 16609825 18775368
MESH:D001714 Bipolar Disorder Carbamazepine 7.5920046352 17594078
MESH:D001714 Bipolar Disorder Valproic Acid 7.5917594078 20046352
MESH:D001778 Blood Coagulation Disorders Tetrachlorodibenzodioxin 3.0712125929
MESH:D001836 Body Weight Changes Tetrachlorodibenzodioxin 3.8515340226
MESH:D001848 Bone Diseases, Developmental Tetrachlorodibenzodioxin 8.0815746008
MESH:D001848 Bone Diseases, Developmental Valproic Acid 8.088888407
MESH:D001943 Breast Neoplasms Benzo(a)pyrene 1.8920146248 17474063
MESH:D001943 Breast Neoplasms Tetrachlorodibenzodioxin 1.8920435547
MESH:D002056 Burns Ethanol 4.6916374292
MESH:D002277 Carcinoma Tetrachlorodibenzodioxin 2.8216835633
MESH:D006528 Carcinoma, Hepatocellular Ethanol 2.4018788625 15763234 15289165
MESH:D002294 Carcinoma, Squamous Cell Benzo(a)pyrene 2.0620419170
MESH:D006332 Cardiomegaly Ethanol 6.8919332462
MESH:D006332 Cardiomegaly Tetrachlorodibenzodioxin 6.8916120746 18850075 18670907
MESH:D002659 Child Development Disorders, Pervasive Valproic Acid 2.7220734317
MESH:D018281 Cholangiocarcinoma Tetrachlorodibenzodioxin 3.1916835633
MESH:D002971 Cleft Lip Ethanol 3.6015513904
MESH:D002972 Cleft Palate Ethanol 5.9915513904
MESH:D002972 Cleft Palate Tetrachlorodibenzodioxin 5.998697196 12621046 15668235 16354765 15340226
MESH:D003092 Colitis Selenium 3.8217936198
MESH:D000013 Congenital Abnormalities Tetrachlorodibenzodioxin 3.0814669216 17141729
MESH:D019465 Craniofacial Abnormalities Carbamazepine 5.509014606
MESH:D019465 Craniofacial Abnormalities Ethanol 5.5019302082 15451040 11873399 11198716 10194807 15513904 15451039
MESH:D019465 Craniofacial Abnormalities Tetrachlorodibenzodioxin 5.5020055451 15322242 10048152
MESH:D019465 Craniofacial Abnormalities Valproic Acid 5.5017688650 16575769 8888407
MESH:D003924 Diabetes Mellitus, Type 2 Tetrachlorodibenzodioxin 1.6717107852
OMIM:607208 DRAVET SYNDROME Carbamazepine 5.4911748493
MESH:D004342 Drug Hypersensitivity Carbamazepine 4.4216538176 16538175 15057820 20216337
MESH:D056486 Drug-Induced Liver Injury Carbamazepine 12.1417465707
MESH:D056486 Drug-Induced Liver Injury Ethanol 12.1411566570
MESH:D056486 Drug-Induced Liver Injury Selenium 12.1415131321
MESH:D056486 Drug-Induced Liver Injury Tetrachlorodibenzodioxin 12.1420420201
MESH:D056486 Drug-Induced Liver Injury Valproic Acid 12.1419641884 1733752
MESH:D004362 Drug Toxicity Carbamazepine 8.4720216337
MESH:D004362 Drug Toxicity Tetrachlorodibenzodioxin 8.4711462148
MESH:D004421 Dystonia Valproic Acid 4.081851702
MESH:D004487 Edema Tetrachlorodibenzodioxin 2.4112711302 11000095
MESH:D004489 Edema, Cardiac Tetrachlorodibenzodioxin 3.9616714409 18230668 15322242
MESH:D004681 Encephalomyelitis, Autoimmune, Experimental Carbamazepine 4.7717654737
MESH:D004715 Endometriosis Tetrachlorodibenzodioxin 3.059294722 10568697
MESH:D004816 Epidermal Necrolysis, Toxic Carbamazepine 5.2916538176 18855540 19915237 16415921 20485159
MESH:D004831 Epilepsies, Myoclonic Carbamazepine 11.3417275665
MESH:D004831 Epilepsies, Myoclonic Valproic Acid 11.343659116 17275665
MESH:D004828 Epilepsies, Partial Carbamazepine 10.5917116037 15008574 16628512
MESH:D004828 Epilepsies, Partial Valproic Acid 10.593922381 16628512
MESH:D004827 Epilepsy Carbamazepine 7.1217465707 17178248 18234410 20417680 19700373 7988514 9014606 19620853 19439326 821787
MESH:D004827 Epilepsy Valproic Acid 7.1218234410 20417680
MESH:D004832 Epilepsy, Absence Valproic Acid 3.617562514 6254150 6426943
MESH:D017029 Epilepsy, Complex Partial Carbamazepine 11.857750514
MESH:D017029 Epilepsy, Complex Partial Valproic Acid 11.857750514
MESH:D004830 Epilepsy, Tonic-Clonic Carbamazepine 11.063659116 15276670
MESH:D004830 Epilepsy, Tonic-Clonic Valproic Acid 11.063659116
MESH:D004916 Erythromelalgia marker/mechanism 17145499 19549232
MESH:D004916 Erythromelalgia Carbamazepine 5.7719549232
MESH:D004938 Esophageal Neoplasms Benzo(a)pyrene 4.6216530937
MESH:D004938 Esophageal Neoplasms Ethanol 4.6216704527
MESH:D005076 Exanthema Carbamazepine 5.5220485159
MESH:D005124 Eye Abnormalities Tetrachlorodibenzodioxin 3.0311564622
MESH:D005234 Fatty Liver Ethanol 13.5819236843 18620774 16409862
MESH:D005234 Fatty Liver Fish Oils 13.5818620774
MESH:D005234 Fatty Liver Valproic Acid 13.5814986274 19224547
MESH:D005235 Fatty Liver, Alcoholic Ethanol 5.7317920746
MESH:D005310 Fetal Alcohol Syndrome Ethanol 5.3515451040 16946407 10194807 15513904
MESH:D005313 Fetal Death Tetrachlorodibenzodioxin 3.5011858732
MESH:D005315 Fetal Diseases Valproic Acid 4.9516575769
MESH:D005317 Fetal Growth Retardation Valproic Acid 4.178888407 18558336
MESH:D005355 Fibrosis Tetrachlorodibenzodioxin 2.9920067830
MESH:D005756 Gastritis Ethanol 4.7615046732
OMIM:604403 GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 2 marker/mechanism
MESH:D006058 Gonadal Disorders Tetrachlorodibenzodioxin 4.6610696789
MESH:D006330 Heart Defects, Congenital Benzo(a)pyrene 6.4920471113
MESH:D006330 Heart Defects, Congenital Tetrachlorodibenzodioxin 6.4910048152 11294989
MESH:D006333 Heart Failure Selenium 3.0917162251
MESH:D006470 Hemorrhage Tetrachlorodibenzodioxin 3.3611000095
MESH:D006529 Hepatomegaly Tetrachlorodibenzodioxin 2.9316120746 15340226 12621046
MESH:D006849 Hydrocephalus Valproic Acid 4.9217688650
MESH:D006869 Hydronephrosis Lithium Chloride 13.2419797860
MESH:D006869 Hydronephrosis Tetrachlorodibenzodioxin 13.2416354765 8697196 18606429 15340226 16959395
MESH:D006930 Hyperalgesia Ethanol 3.7418783367
MESH:D020138 Hyperhomocysteinemia Carbamazepine 4.7510459572
MESH:D006949 Hyperlipidemias Fish Oils 4.7915752949
MESH:D006965 Hyperplasia Carbamazepine 5.2518773962
MESH:D006968 Hypersensitivity, Delayed Fish Oils 5.5711484837
MESH:D006973 Hypertension Tetrachlorodibenzodioxin 1.9118670907 18850075
OMIM:243000 INDIFFERENCE TO PAIN, CONGENITAL, AUTOSOMAL RECESSIVE marker/mechanism
MESH:D007249 Inflammation Tetrachlorodibenzodioxin 1.8712878042 12200463
MESH:D007251 Influenza, Human Selenium 4.2616624496
MESH:D007569 Jaw Abnormalities Ethanol 10.2215513904
MESH:D007569 Jaw Abnormalities Tetrachlorodibenzodioxin 10.2216580747
MESH:D007676 Kidney Failure, Chronic Selenium 3.9116518626
MESH:D007683 Kidney Tubular Necrosis, Acute Calcium 5.1116316344
MESH:D007859 Learning Disorders Ethanol 4.2515451040
MESH:D015470 Leukemia, Myeloid, Acute Valproic Acid 2.1516294345 17596541
MESH:D017880 Limb Deformities, Congenital Ethanol 3.8317676605
MESH:D008103 Liver Cirrhosis Ethanol 3.3915289165
MESH:D008104 Liver Cirrhosis, Alcoholic Ethanol 5.1518295389
MESH:D008106 Liver Cirrhosis, Experimental Ethanol 2.5018166357
MESH:D008106 Liver Cirrhosis, Experimental Tetrachlorodibenzodioxin 2.5012878042
MESH:D008108 Liver Diseases, Alcoholic Ethanol 4.6917347304 17207112
MESH:D008113 Liver Neoplasms Benzo(a)pyrene 4.3621137059 20195826
MESH:D008113 Liver Neoplasms Tetrachlorodibenzodioxin 4.3616984957
MESH:D008114 Liver Neoplasms, Experimental Tetrachlorodibenzodioxin 2.1212151625
MESH:D017563 Lung Diseases, Interstitial Valproic Acid 4.3217228818
MESH:D008175 Lung Neoplasms Benzo(a)pyrene 2.1920464547 18520028 20064080 18816296 17053015 20869020 6695378 20135361 18569708
MESH:D008175 Lung Neoplasms Tetrachlorodibenzodioxin 2.1919555203 11884234
MESH:D008180 Lupus Erythematosus, Systemic Carbamazepine 3.5716628512
MESH:D008325 Mammary Neoplasms, Experimental Selenium 2.7815318939
MESH:D008569 Memory Disorders Ethanol 4.2218411066 15451040
MESH:D008607 Mental Retardation Carbamazepine 3.739014606
MESH:D008654 Mesothelioma Selenium 2.8015107826
MESH:D008881 Migraine Disorders Valproic Acid 3.2118803445 18765137
MESH:D009062 Mouth Neoplasms Benzo(a)pyrene 3.2116381670
MESH:D009139 Musculoskeletal Abnormalities Valproic Acid 4.068888407
MESH:D009190 Myelodysplastic Syndromes Valproic Acid 3.1717596541
MESH:D017202 Myocardial Ischemia Tetrachlorodibenzodioxin 3.0412213967
MESH:D009224 Myotonia Congenita Carbamazepine 5.5220399394
MESH:D009369 Neoplasms Benzo(a)pyrene 2.1811141357
MESH:D009421 Nervous System Malformations Carbamazepine 10.0516990009
MESH:D009421 Nervous System Malformations Tetrachlorodibenzodioxin 10.0514600291
MESH:D009436 Neural Tube Defects Valproic Acid 3.1416359493 8888407
MESH:D010018 Osteomalacia Carbamazepine 5.5217016548
MESH:D010024 Osteoporosis Calcium 3.8017882678
MESH:D010146 Pain Carbamazepine 4.0615215642
MESH:D010190 Pancreatic Neoplasms Ethanol 2.9812384795
MESH:D010267 Parapsoriasis Carbamazepine 5.7416538176
OMIM:167400 PAROXYSMAL EXTREME PAIN DISORDER marker/mechanism 17145499 17679678
OMIM:167400 PAROXYSMAL EXTREME PAIN DISORDER Carbamazepine 5.9717679678 17145499
MESH:D010382 Peliosis Hepatis Tetrachlorodibenzodioxin 4.3112520081
MESH:D010954 Plasmacytoma Selenium 4.9515087411
MESH:D011141 Polyuria Lithium Chloride 6.0519692487
MESH:D017119 Porphyria Cutanea Tarda Tetrachlorodibenzodioxin 3.5918163543
MESH:D011248 Pregnancy Complications Carbamazepine 5.199014606
MESH:D011297 Prenatal Exposure Delayed Effects Carbamazepine 16.689014606
MESH:D011297 Prenatal Exposure Delayed Effects Tetrachlorodibenzodioxin 16.6811896295 11222880 11118676 11399792
MESH:D011297 Prenatal Exposure Delayed Effects Valproic Acid 16.6820603192
MESH:D011471 Prostatic Neoplasms Benzo(a)pyrene 2.9717292933
MESH:D019310 Pseudolymphoma Carbamazepine 12.8112752131 9591791
MESH:D019310 Pseudolymphoma Valproic Acid 12.8112752131 11422049
MESH:D015619 Respiratory System Abnormalities Tetrachlorodibenzodioxin 3.8718990726
MESH:D012208 Rhabdomyosarcoma Valproic Acid 4.2119155313
MESH:D012559 Schizophrenia Valproic Acid 2.0715737665 19110320
MESH:D012640 Seizures Carbamazepine 10.1915946322 9046859 19414003 9844417 16938433 16876388 16180713
MESH:D012640 Seizures Ethanol 10.199754883
MESH:D012640 Seizures Valproic Acid 10.1916876388 1511512 11738929 17978042 15475178 11044598 14763951 3137016
MESH:D012878 Skin Neoplasms Benzo(a)pyrene 5.5110029692 19755658
MESH:D012878 Skin Neoplasms Tetrachlorodibenzodioxin 5.5116192470
MESH:D012893 Sleep Disorders Carbamazepine 5.1719414003
MESH:D016135 Spinal Dysraphism Valproic Acid 3.8019490988
MESH:D013226 Status Epilepticus Valproic Acid 4.6012833885
MESH:D013262 Stevens-Johnson Syndrome Carbamazepine 5.2515057820 18855540 19915237 16415921 16538176 20485159 19694795
MESH:D013274 Stomach Neoplasms Benzo(a)pyrene 2.542093021 20155912
MESH:D013274 Stomach Neoplasms Ethanol 2.5418456281
MESH:D013276 Stomach Ulcer Ethanol 3.5616755016 9562338 17918041 11906479 17189318 9211565
MESH:D013375 Substance Withdrawal Syndrome Ethanol 4.289754883
MESH:D013959 Thyroid Diseases Tetrachlorodibenzodioxin 3.9612697716
MESH:D014178 Translocation, Genetic Valproic Acid 5.3017262798
MESH:D020194 Unverricht-Lundborg Syndrome Valproic Acid 4.573119515
MESH:D001749 Urinary Bladder Neoplasms Benzo(a)pyrene 2.1917053015
MESH:D014564 Urogenital Abnormalities Valproic Acid 4.688888407
MESH:D054079 Vascular Malformations Tetrachlorodibenzodioxin 4.6612125929
MESH:D019282 Wasting Syndrome Tetrachlorodibenzodioxin 4.3115886252
Pathway ID Pathway Name
REACT:18266 Axon guidance
Pharmacogenomics Knowledge Base Top
Drug Bank Top
Drugbank ID Action Drug Name Description
DB00243 antagonist Ranolazine Enzyme Inhibitors
DB00281 antagonist Xylonor Spray Antiarrhythmic Agents;Anesthetics;Anesthetics, Local;Anti-Arrhythmia Agents
DB00909 antagonist Zonisamide Antioxidants;Anticonvulsants
No data
No data
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Simple Query:


  (e.g. CHD8)

Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 1,036
  • Genes: 1,379
  • CNVs/SVs: 5,420
  • SNVs/Indels: 11,669
  • de novo Mutations: 5,669
  • Mosaics: 789
  • Linkage Regions: 172
  • Paper Collected: 6/30/2018
  • Last Update: 8/26/2018


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