AutismKB 2.0

Annotation Detail for SCN1A


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Basic Information Top
Gene Symbol:SCN1A ( FEB3,FEB3A,GEFSP2,HBSCI,NAC1,Nav1.1,SCN1,SMEI )
Gene Full Name: sodium channel, voltage-gated, type I, alpha subunit
Band: 2q24.3
Quick LinksEntrez ID:6323; OMIM: 182389; Uniprot ID:SCN1A_HUMAN; ENSEMBL ID: ENSG00000144285; HGNC ID: 10585
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 
fetus2 / 5640123
neonate0 / 310970 
infant1 / 2362042
juvenile0 / 555560 
adult10 / 19391215
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 
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 
leukemia0 / 958420 
liver tumor0 / 963590 
lung tumor0 / 1031270 
lymphoma0 / 717550 
non-neoplasia0 / 972500 
normal46 / 336030713
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 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 
bone0 / 716550 
bone marrow0 / 488010 
brain33 / 110098929
cervix0 / 481710 
connective tissue0 / 1492550 
ear0 / 162120 
embryonic tissue0 / 2157220 
esophagus0 / 202090 
eye2 / 2110549
heart0 / 896260 
intestine0 / 2344720 
kidney0 / 2117770 
larynx0 / 241450 
liver0 / 2077430 
lung0 / 3369740 
lymph0 / 442700 
lymph node0 / 916100 
mammary gland0 / 1532710 
mouth0 / 670520 
muscle3 / 10771527
nerve0 / 157680 
ovary0 / 1020510 
pancreas0 / 2148120 
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta0 / 2808250 
prostate0 / 1893450 
salivary gland0 / 201550 
skin0 / 2105740 
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: 210383_at
Cell line Expression level Expression bar
721_B_lymphoblasts7.85
Adipocyte6.9
AdrenalCortex9.6
Adrenalgland6.35
Amygdala28
Appendix10.25
AtrioventricularNode7
BDCA4+_DentriticCells7.15
Bonemarrow7.8
BronchialEpithelialCells6.6
CD105+_Endothelial7.05
CD14+_Monocytes7.7
CD19+_BCells(neg._sel.)7.15
CD33+_Myeloid8.9
CD34+8.25
CD4+_Tcells7.3
CD56+_NKCells7.8
CD71+_EarlyErythroid6.95
CD8+_Tcells6.15
CardiacMyocytes10.65
Caudatenucleus14.95
Cerebellum6
CerebellumPeduncles9.2
CiliaryGanglion8.8
CingulateCortex42.7
Colorectaladenocarcinoma7.35
DorsalRootGanglion6.3
FetalThyroid7.3
Fetalbrain44.55
Fetalliver6.35
Fetallung5.45
GlobusPallidus7.55
Heart14
Hypothalamus33.8
Kidney6.3
Leukemia_chronicMyelogenousK-5626.35
Leukemia_promyelocytic-HL-606.45
Leukemialymphoblastic(MOLT-4)5.65
Liver10.3
Lung7.8
Lymphnode6.1
Lymphoma_burkitts(Daudi)10.45
Lymphoma_burkitts(Raji)11.45
MedullaOblongata51.2
OccipitalLobe25.25
OlfactoryBulb5.55
Ovary5.1
Pancreas6.15
PancreaticIslet7.8
ParietalLobe13.2
Pituitary8.4
Placenta7.7
Pons7.85
PrefrontalCortex161.75
Prostate8.1
Salivarygland6.2
SkeletalMuscle9.5
Skin6.4
SmoothMuscle8.5
Spinalcord10
SubthalamicNucleus35.6
SuperiorCervicalGanglion10.15
TemporalLobe36.9
Testis6.2
TestisGermCell5.95
TestisIntersitial6.3
TestisLeydigCell7.45
TestisSeminiferousTubule6.15
Thalamus43.9
Thymus5.25
Thyroid8.65
Tongue7.55
Tonsil7.2
Trachea5.9
TrigeminalGanglion8.65
Uterus5.65
UterusCorpus7.15
WholeBlood7.75
Wholebrain17.55
colon7
pineal_day11.4
pineal_night10.22
retina8.8
small_intestine6.65
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_546_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
Amygdala6.57 ± 0.47
Basal Forebrain6.62 ± 0.45
Basal Part of Pons7.44 ± 0.11
Cerebellar Cortex6.6 ± 0.34
Cerebellar Nuclei7.25 ± 0.22
Claustrum6.93 ± 0.62
Epithalamus6.82 ± 0.63
Frontal Lobe6.91 ± 0.47
Globus Pallidus6.82 ± 0.3
Hypothalamus6.43 ± 0.39
Insula6.52 ± 0.39
Limbic Lobe6.78 ± 0.37
Mesencephalon6.67 ± 0.41
Myelencephalon6.83 ± 0.45
Occipital Lobe7.3 ± 0.31
Parietal Lobe7.16 ± 0.39
Pontine Tegmentum6.87 ± 0.42
Striatum6.8 ± 0.37
Subthalamus7.5 ± 0.15
Temporal Lobe6.77 ± 0.44
Thalamus7.18 ± 0.4
White Matter5.32 ± 0.23
Mouse Brain ISH
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00070342 12 1862 1873 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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