AutismKB 2.0

Annotation Detail for SCN2A


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Basic Information Top
Gene Symbol:SCN2A ( BFIC3,HBA,HBSCI,HBSCII,NAC2,Na(v)1.2,Nav1.2,SCN2A1,SCN2A2 )
Gene Full Name: sodium channel, voltage-gated, type II, alpha subunit
Band: 2q24.3
Quick LinksEntrez ID:6326; OMIM: 182390; Uniprot ID:SCN2A_HUMAN; ENSEMBL ID: ENSG00000136531; HGNC ID: 10588
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 
fetus16 / 56401228
neonate0 / 310970 
infant0 / 236200 
juvenile1 / 5555617
adult40 / 193912120
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 
chondrosarcoma3 / 8282336
colorectal tumor1 / 1142468
esophageal tumor0 / 172900 
gastrointestinal tumor0 / 1193690 
germ cell tumor3 / 26384511
glioma0 / 1068830 
head and neck tumor0 / 1363020 
kidney tumor2 / 6895929
leukemia0 / 958420 
liver tumor0 / 963590 
lung tumor0 / 1031270 
lymphoma0 / 717550 
non-neoplasia7 / 9725071
normal90 / 336030726
ovarian tumor0 / 766820 
pancreatic tumor0 / 1046160 
primitive neuroectodermal tumor of the CNS1 / 1256807
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 
bone2 / 7165527
bone marrow0 / 488010 
brain81 / 110098973
cervix0 / 481710 
connective tissue2 / 14925513
ear0 / 162120 
embryonic tissue0 / 2157220 
esophagus0 / 202090 
eye5 / 21105423
heart0 / 896260 
intestine1 / 2344724
kidney8 / 21177737
larynx0 / 241450 
liver0 / 2077430 
lung14 / 33697441
lymph0 / 442700 
lymph node0 / 916100 
mammary gland0 / 1532710 
mouth0 / 670520 
muscle5 / 10771546
nerve0 / 157680 
ovary1 / 1020519
pancreas2 / 2148129
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta0 / 2808250 
prostate0 / 1893450 
salivary gland0 / 201550 
skin0 / 2105740 
spleen0 / 539520 
stomach0 / 966190 
testis2 / 3304426
thymus0 / 811310 
thyroid0 / 474730 
tonsil0 / 169990 
trachea0 / 524130 
umbilical cord0 / 136800 
uterus0 / 2328780 
vascular1 / 5178019
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 206381_at
Cell line Expression level Expression bar
721_B_lymphoblasts6.65
Adipocyte5.35
AdrenalCortex8.45
Adrenalgland4.5
Amygdala17.9
Appendix5.5
AtrioventricularNode4.2
BDCA4+_DentriticCells5.3
Bonemarrow5.3
BronchialEpithelialCells5.25
CD105+_Endothelial5.55
CD14+_Monocytes5.35
CD19+_BCells(neg._sel.)5.85
CD33+_Myeloid7
CD34+7.3
CD4+_Tcells5.95
CD56+_NKCells6.2
CD71+_EarlyErythroid5
CD8+_Tcells5
CardiacMyocytes6.85
Caudatenucleus6.2
Cerebellum21
CerebellumPeduncles44.5
CiliaryGanglion3.9
CingulateCortex38.3
Colorectaladenocarcinoma5.45
DorsalRootGanglion4.2
FetalThyroid5.4
Fetalbrain43.75
Fetalliver4.65
Fetallung4.3
GlobusPallidus41.35
Heart6.8
Hypothalamus6.15
Kidney4.45
Leukemia_chronicMyelogenousK-5624.9
Leukemia_promyelocytic-HL-604.75
Leukemialymphoblastic(MOLT-4)4.35
Liver7.15
Lung5.95
Lymphnode4.7
Lymphoma_burkitts(Daudi)6.9
Lymphoma_burkitts(Raji)7.55
MedullaOblongata22.85
OccipitalLobe51.9
OlfactoryBulb7.85
Ovary3.6
Pancreas4.35
PancreaticIslet5.7
ParietalLobe38.15
Pituitary6.35
Placenta5.45
Pons12.55
PrefrontalCortex22.05
Prostate6.25
Salivarygland4.35
SkeletalMuscle9.1
Skin4.2
SmoothMuscle6.2
Spinalcord5.8
SubthalamicNucleus42.95
SuperiorCervicalGanglion6.45
TemporalLobe18.05
Testis4.7
TestisGermCell4.55
TestisIntersitial4.5
TestisLeydigCell5.4
TestisSeminiferousTubule4.9
Thalamus5.45
Thymus4.25
Thyroid6.8
Tongue5.55
Tonsil5.2
Trachea4.55
TrigeminalGanglion8.95
Uterus4.45
UterusCorpus6.5
WholeBlood5.95
Wholebrain9.4
colon5.45
pineal_day8
pineal_night7.38
retina6.45
small_intestine5.15
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_548_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
Amygdala10.36 ± 0.45
Basal Forebrain9.99 ± 0.31
Basal Part of Pons10.24 ± 0.48
Cerebellar Cortex10.71 ± 0.12
Cerebellar Nuclei8.88 ± 0.59
Claustrum10.6 ± 0.23
Epithalamus9.03 ± 0.99
Frontal Lobe10.27 ± 0.49
Globus Pallidus7.93 ± 0.85
Hypothalamus10.22 ± 0.69
Insula10.39 ± 0.2
Limbic Lobe10.47 ± 0.56
Mesencephalon9.96 ± 0.65
Myelencephalon9.98 ± 0.74
Occipital Lobe9.6 ± 0.72
Parietal Lobe10.1 ± 0.52
Pontine Tegmentum9.99 ± 0.77
Striatum9.3 ± 0.66
Subthalamus9.35 ± 0.52
Temporal Lobe10.45 ± 0.44
Thalamus9.86 ± 0.56
White Matter7.75 ± 0.44
Mouse Brain ISH
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00070342 12 1852 1863 IHCLDILFAFTK Peptide Atlas
SCN2A_HUMAN_998 12 998 1009 NEMNNLQIAVGR PRIDE

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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