AutismKB 2.0

Annotation Detail for SCN4A


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Basic Information Top
Gene Symbol:SCN4A ( HOKPP2,HYKPP,HYPP,NAC1A,Na(V)1.4,Nav1.4,SkM1 )
Gene Full Name: sodium channel, voltage-gated, type IV, alpha subunit
Band: 17q23.3
Quick LinksEntrez ID:6329; OMIM: 603967; Uniprot ID:SCN4A_HUMAN; ENSEMBL ID: ENSG00000007314; HGNC ID: 10591
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 
fetus3 / 5640125
neonate0 / 310970 
infant0 / 236200 
juvenile0 / 555560 
adult8 / 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) tumor1 / 9417810
cervical tumor0 / 343660 
chondrosarcoma0 / 828230 
colorectal tumor0 / 1142460 
esophageal tumor0 / 172900 
gastrointestinal tumor0 / 1193690 
germ cell tumor0 / 2638450 
glioma0 / 1068830 
head and neck tumor0 / 1363020 
kidney tumor0 / 689590 
leukemia3 / 9584231
liver tumor0 / 963590 
lung tumor1 / 1031279
lymphoma0 / 717550 
non-neoplasia0 / 972500 
normal13 / 33603073
ovarian tumor0 / 766820 
pancreatic tumor0 / 1046160 
primitive neuroectodermal tumor of the CNS0 / 1256800 
prostate cancer0 / 1026800 
retinoblastoma0 / 463560 
skin tumor0 / 1249490 
soft tissue/muscle tissue tumor1 / 1251917
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 
bone0 / 716550 
bone marrow0 / 488010 
brain1 / 11009890 
cervix0 / 481710 
connective tissue0 / 1492550 
ear0 / 162120 
embryonic tissue0 / 2157220 
esophagus0 / 202090 
eye0 / 2110540 
heart0 / 896260 
intestine0 / 2344720 
kidney0 / 2117770 
larynx1 / 2414541
liver1 / 2077434
lung1 / 3369742
lymph0 / 442700 
lymph node3 / 9161032
mammary gland1 / 1532716
mouth0 / 670520 
muscle4 / 10771537
nerve0 / 157680 
ovary0 / 1020510 
pancreas0 / 2148120 
parathyroid0 / 205390 
pharynx1 / 4132824
pituitary gland1 / 1658560
placenta2 / 2808257
prostate0 / 1893450 
salivary gland0 / 201550 
skin0 / 2105740 
spleen0 / 539520 
stomach0 / 966190 
testis1 / 3304423
thymus0 / 811310 
thyroid1 / 4747321
tonsil0 / 169990 
trachea1 / 5241319
umbilical cord0 / 136800 
uterus0 / 2328780 
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 206981_at
Cell line Expression level Expression bar
721_B_lymphoblasts4.8
Adipocyte3.8
AdrenalCortex4.1
Adrenalgland3.35
Amygdala4.05
Appendix4.35
AtrioventricularNode3.25
BDCA4+_DentriticCells4.25
Bonemarrow4.6
BronchialEpithelialCells3.8
CD105+_Endothelial3.9
CD14+_Monocytes4.1
CD19+_BCells(neg._sel.)4.45
CD33+_Myeloid4.95
CD34+4.9
CD4+_Tcells4.2
CD56+_NKCells4.6
CD71+_EarlyErythroid3.65
CD8+_Tcells3.75
CardiacMyocytes4.95
Caudatenucleus3.45
Cerebellum3.15
CerebellumPeduncles4.5
CiliaryGanglion2.8
CingulateCortex4
Colorectaladenocarcinoma3.85
DorsalRootGanglion3.1
FetalThyroid3.75
Fetalbrain3.85
Fetalliver3.4
Fetallung3.2
GlobusPallidus3
Heart4.95
Hypothalamus4.2
Kidney3.35
Leukemia_chronicMyelogenousK-5623.45
Leukemia_promyelocytic-HL-603.4
Leukemialymphoblastic(MOLT-4)3.1
Liver5.15
Lung4.2
Lymphnode3.3
Lymphoma_burkitts(Daudi)4.95
Lymphoma_burkitts(Raji)5.4
MedullaOblongata3.55
OccipitalLobe3.45
OlfactoryBulb3.05
Ovary2.75
Pancreas3.15
PancreaticIslet4.15
ParietalLobe4.15
Pituitary4.55
Placenta4
Pons3.7
PrefrontalCortex4.8
Prostate4.5
Salivarygland3.15
SkeletalMuscle7.35
Skin3.3
SmoothMuscle4.35
Spinalcord4.15
SubthalamicNucleus3.55
SuperiorCervicalGanglion4.65
TemporalLobe3.7
Testis3.3
TestisGermCell3.15
TestisIntersitial3.35
TestisLeydigCell3.85
TestisSeminiferousTubule3.3
Thalamus3.95
Thymus3
Thyroid4.9
Tongue4.15
Tonsil3.8
Trachea3.2
TrigeminalGanglion4.35
Uterus3.15
UterusCorpus3.5
WholeBlood4.2
Wholebrain3.25
colon3.9
pineal_day4.86
pineal_night4.74
retina4.675
small_intestine3.75
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_14630_PI416261804
  • 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
Amygdala2.13 ± 0.93
Basal Forebrain1.52 ± 0.34
Basal Part of Pons1.5 ± 0.55
Cerebellar Cortex1.58 ± 0.74
Cerebellar Nuclei1.91 ± 0.74
Claustrum2.31 ± 0.83
Epithalamus1.35 ± 0.68
Frontal Lobe1.59 ± 0.75
Globus Pallidus2.43 ± 0.9
Hypothalamus1.61 ± 0.71
Insula1.39 ± 0.37
Limbic Lobe1.84 ± 0.75
Mesencephalon1.91 ± 0.74
Myelencephalon1.8 ± 0.77
Occipital Lobe1.81 ± 0.78
Parietal Lobe1.77 ± 0.88
Pontine Tegmentum1.52 ± 0.72
Striatum1.75 ± 0.79
Subthalamus1.57 ± 0.69
Temporal Lobe1.57 ± 0.71
Thalamus1.57 ± 0.72
White Matter2.08 ± 0.41
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Scn4aCBCerebellum14.9
15.7
Scn4aCTXCerebral cortex32.7
23.45
Scn4aHIPHippocampal region15.3
16.18
Scn4aHPFHippocampal formation19.02
17.31
Scn4aHYHypothalamus12.56
8.83
Scn4aLSXLateral septal complex4.97
3.05
Scn4aMBMidbrain12.93
10.54
Scn4aMYMedulla31.91
31.42
Scn4aOLFOlfactory bulb40.39
31.74
Scn4aPPons22.51
21.21
Scn4aPALPallidum28.04
24.84
Scn4aRHPRetrohippocampal region27.87
20.65
Scn4asAMYStriatum-like amygdalar nuclei32.78
26.38
Scn4aSTRStriatum27.64
19.76
Scn4aSTRdStriatum dorsal region26.45
17.94
Scn4aSTRvStriatum ventral region39.73
29.28
Scn4aTHThalamus23.6
16.8
Peptide Top

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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