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
Unigene EST Top
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
embryoid body0 / 707610 
blastocyst0 / 623190 
fetus10 / 56401217
neonate0 / 310970 
infant1 / 2362042
juvenile5 / 5555689
adult9 / 19391214
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor0 / 127940 
bladder carcinoma0 / 174750 
breast (mammary gland) tumor0 / 941780 
cervical tumor0 / 343660 
chondrosarcoma2 / 8282324
colorectal tumor0 / 1142460 
esophageal tumor0 / 172900 
gastrointestinal tumor0 / 1193690 
germ cell tumor0 / 2638450 
glioma0 / 1068830 
head and neck tumor1 / 1363027
kidney tumor0 / 689590 
leukemia0 / 958420 
liver tumor2 / 9635920
lung tumor1 / 1031279
lymphoma0 / 717550 
non-neoplasia1 / 9725010
normal18 / 33603075
ovarian tumor0 / 766820 
pancreatic tumor0 / 1046160 
primitive neuroectodermal tumor of the CNS10 / 12568079
prostate cancer0 / 1026800 
retinoblastoma0 / 463560 
skin tumor0 / 1249490 
soft tissue/muscle tissue tumor0 / 1251910 
uterine tumor0 / 902570 
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland0 / 331970 
ascites0 / 400150 
bladder0 / 297570 
blood0 / 1234780 
bone1 / 7165513
bone marrow0 / 488010 
brain4 / 11009893
cervix0 / 481710 
connective tissue2 / 14925513
ear0 / 162120 
embryonic tissue0 / 2157220 
esophagus0 / 202090 
eye3 / 21105414
heart0 / 896260 
intestine0 / 2344720 
kidney0 / 2117770 
larynx0 / 241450 
liver2 / 2077439
lung3 / 3369748
lymph0 / 442700 
lymph node0 / 916100 
mammary gland0 / 1532710 
mouth1 / 6705214
muscle0 / 1077150 
nerve1 / 1576863
ovary0 / 1020510 
pancreas0 / 2148120 
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta3 / 28082510
prostate0 / 1893450 
salivary gland0 / 201550 
skin1 / 2105744
spleen0 / 539520 
stomach0 / 966190 
testis0 / 3304420 
thymus0 / 811310 
thyroid0 / 474730 
tonsil0 / 169990 
trachea0 / 524130 
umbilical cord0 / 136800 
uterus0 / 2328780 
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 206950_at
Cell line Expression level Expression bar
721_B_lymphoblasts10.8
Adipocyte10.5
AdrenalCortex16.55
Adrenalgland11
Amygdala9.95
Appendix15.05
AtrioventricularNode19
BDCA4+_DentriticCells14.55
Bonemarrow11.5
BronchialEpithelialCells10
CD105+_Endothelial10.65
CD14+_Monocytes14.35
CD19+_BCells(neg._sel.)11.1
CD33+_Myeloid13.6
CD34+12.1
CD4+_Tcells10.4
CD56+_NKCells11.35
CD71+_EarlyErythroid10.55
CD8+_Tcells9.2
CardiacMyocytes26.45
Caudatenucleus9.9
Cerebellum9
CerebellumPeduncles15.25
CiliaryGanglion21.6
CingulateCortex11.95
Colorectaladenocarcinoma10.45
DorsalRootGanglion17.85
FetalThyroid13.35
Fetalbrain11.25
Fetalliver9.5
Fetallung7.5
GlobusPallidus9.9
Heart22.2
Hypothalamus11.4
Kidney11.15
Leukemia_chronicMyelogenousK-5629.6
Leukemia_promyelocytic-HL-608.95
Leukemialymphoblastic(MOLT-4)8.05
Liver20.35
Lung11.9
Lymphnode8.4
Lymphoma_burkitts(Daudi)15.8
Lymphoma_burkitts(Raji)17.95
MedullaOblongata9.95
OccipitalLobe9.95
OlfactoryBulb8.45
Ovary10.4
Pancreas9.9
PancreaticIslet11.45
ParietalLobe13.4
Pituitary14.1
Placenta10.3
Pons12.3
PrefrontalCortex11.95
Prostate12.25
Salivarygland11.25
SkeletalMuscle20.9
Skin22.8
SmoothMuscle12.4
Spinalcord11.35
SubthalamicNucleus11.35
SuperiorCervicalGanglion21.55
TemporalLobe11.15
Testis9.25
TestisGermCell12.4
TestisIntersitial14.1
TestisLeydigCell12.4
TestisSeminiferousTubule18.8
Thalamus11.9
Thymus7.65
Thyroid12
Tongue14.3
Tonsil11.35
Trachea8.7
TrigeminalGanglion22.85
Uterus8.15
UterusCorpus12.6
WholeBlood11.85
Wholebrain7.95
colon10.55
pineal_day12.3
pineal_night12.14
retina13.15
small_intestine9.75
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_557_PI416408490
  • Donor H0351.2001
  • Sex: Male     Age: 24 years     Race/Ethnicity: African American     Handedness: Left
  • Tissue Receipt Date: 7/29/2009     Serology: Pass      Tissue pH :6.72     Additional Medical Information :History of asthma
  • Postmortem Interval: 23 hours (estimated time of death to time that tissue is frozen)
  • Toxicology: Positive for atropine and caffeine, at levels usually not toxicologically significant
Tissue Expression(mean ± stddev) Expression Bar
Amygdala3.77 ± 0.82
Basal Forebrain4.43 ± 0.76
Basal Part of Pons1.81 ± 0.5
Cerebellar Cortex2.32 ± 0.53
Cerebellar Nuclei2.51 ± 0.96
Claustrum3.9 ± 0.81
Epithalamus4.6 ± 0.75
Frontal Lobe2.66 ± 0.95
Globus Pallidus3.08 ± 0.81
Hypothalamus4.92 ± 0.46
Insula4.08 ± 0.86
Limbic Lobe3.33 ± 1.26
Mesencephalon3.68 ± 0.96
Myelencephalon3.18 ± 1.19
Occipital Lobe2.82 ± 0.93
Parietal Lobe2.7 ± 1.25
Pontine Tegmentum3.24 ± 1.07
Striatum3.9 ± 1.24
Subthalamus2.04 ± 0.65
Temporal Lobe3.08 ± 0.98
Thalamus2.61 ± 0.74
White Matter2.84 ± 0.41
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Scn9aCBCerebellum2.54
3.01
Scn9aCTXCerebral cortex0.97
1
Scn9aHIPHippocampal region0.71
0.82
Scn9aHPFHippocampal formation0.91
0.88
Scn9aHYHypothalamus0.12
0.11
Scn9aLSXLateral septal complex0.26
0.31
Scn9aMBMidbrain0.68
1.27
Scn9aMYMedulla1.43
1.87
Scn9aOLFOlfactory bulb0.88
0.72
Scn9aPPons0.58
0.68
Scn9aPALPallidum0.18
0.22
Scn9aRHPRetrohippocampal region1.26
0.95
Scn9asAMYStriatum-like amygdalar nuclei0.32
0.28
Scn9aSTRStriatum0.26
0.32
Scn9aSTRdStriatum dorsal region0.26
0.25
Scn9aSTRvStriatum ventral region0.33
0.66
Scn9aTHThalamus0.25
0.21
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00070342 12 1825 1836 IHCLDILFAFTK Peptide Atlas

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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