AutismKB 2.0

Annotation Detail for SCN5A


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Basic Information Top
Gene Symbol:SCN5A ( CDCD2,CMD1E,CMPD2,HB1,HB2,HBBD,HH1,ICCD,IVF,LQT3,Nav1.5,PFHB1,SSS1,VF1 )
Gene Full Name: sodium channel, voltage-gated, type V, alpha subunit
Band: 3p22.2
Quick LinksEntrez ID:6331; OMIM: 600163; Uniprot ID:SCN5A_HUMAN; ENSEMBL ID: ENSG00000183873; HGNC ID: 10593
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 
fetus1 / 5640121
neonate0 / 310970 
infant1 / 2362042
juvenile0 / 555560 
adult2 / 19391211
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 tumor3 / 26384511
glioma0 / 1068830 
head and neck tumor0 / 1363020 
kidney tumor0 / 689590 
leukemia0 / 958420 
liver tumor0 / 963590 
lung tumor0 / 1031270 
lymphoma0 / 717550 
non-neoplasia0 / 972500 
normal6 / 33603071
ovarian tumor3 / 7668239
pancreatic tumor0 / 1046160 
primitive neuroectodermal tumor of the CNS3 / 12568023
prostate cancer0 / 1026800 
retinoblastoma0 / 463560 
skin tumor0 / 1249490 
soft tissue/muscle tissue tumor1 / 1251917
uterine tumor1 / 9025711
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 
blood1 / 1234788
bone0 / 716550 
bone marrow0 / 488010 
brain1 / 11009890 
cervix0 / 481710 
connective tissue0 / 1492550 
ear0 / 162120 
embryonic tissue1 / 2157224
esophagus0 / 202090 
eye1 / 2110544
heart2 / 8962622
intestine0 / 2344720 
kidney0 / 2117770 
larynx0 / 241450 
liver0 / 2077430 
lung0 / 3369740 
lymph0 / 442700 
lymph node0 / 916100 
mammary gland0 / 1532710 
mouth0 / 670520 
muscle0 / 1077150 
nerve0 / 157680 
ovary6 / 10205158
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 
uterus2 / 2328788
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 207413_s_at
Cell line Expression level Expression bar
721_B_lymphoblasts6.1
Adipocyte4.7
AdrenalCortex5.3
Adrenalgland4.05
Amygdala4.9
Appendix4.75
AtrioventricularNode3.9
BDCA4+_DentriticCells5.2
Bonemarrow4.85
BronchialEpithelialCells4.65
CD105+_Endothelial4.75
CD14+_Monocytes5.1
CD19+_BCells(neg._sel.)5.15
CD33+_Myeloid6.2
CD34+6.2
CD4+_Tcells5.75
CD56+_NKCells5.6
CD71+_EarlyErythroid4.45
CD8+_Tcells4.65
CardiacMyocytes6.7
Caudatenucleus4.25
Cerebellum3.85
CerebellumPeduncles5.35
CiliaryGanglion3.6
CingulateCortex4.85
Colorectaladenocarcinoma9.05
DorsalRootGanglion3.8
FetalThyroid4.6
Fetalbrain4.65
Fetalliver4.2
Fetallung3.9
GlobusPallidus3.5
Heart38.45
Hypothalamus5.25
Kidney3.75
Leukemia_chronicMyelogenousK-5624.3
Leukemia_promyelocytic-HL-604.2
Leukemialymphoblastic(MOLT-4)3.85
Liver6.45
Lung5.2
Lymphnode4.15
Lymphoma_burkitts(Daudi)6.2
Lymphoma_burkitts(Raji)7
MedullaOblongata4.3
OccipitalLobe4.2
OlfactoryBulb3.8
Ovary3.2
Pancreas3.9
PancreaticIslet5.05
ParietalLobe5
Pituitary5.55
Placenta4.9
Pons4.5
PrefrontalCortex5.9
Prostate5.65
Salivarygland3.9
SkeletalMuscle5.95
Skin3.7
SmoothMuscle5.3
Spinalcord5.05
SubthalamicNucleus4.3
SuperiorCervicalGanglion5.65
TemporalLobe4.3
Testis4.1
TestisGermCell3.8
TestisIntersitial4
TestisLeydigCell4.65
TestisSeminiferousTubule4.05
Thalamus4.8
Thymus3.7
Thyroid6.05
Tongue4.85
Tonsil4.7
Trachea4
TrigeminalGanglion5.05
Uterus3.95
UterusCorpus4.4
WholeBlood5.25
Wholebrain3.95
colon4.8
pineal_day6.44
pineal_night6.72
retina5.825
small_intestine4.6
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_554_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
Amygdala3.47 ± 0.93
Basal Forebrain3.52 ± 1.12
Basal Part of Pons2.12 ± 0.76
Cerebellar Cortex2.44 ± 0.93
Cerebellar Nuclei2.62 ± 0.8
Claustrum2.99 ± 0.81
Epithalamus2.17 ± 1.07
Frontal Lobe2.1 ± 0.7
Globus Pallidus2.36 ± 0.58
Hypothalamus2.76 ± 0.6
Insula2.17 ± 0.84
Limbic Lobe2.48 ± 0.72
Mesencephalon2.71 ± 0.92
Myelencephalon2.54 ± 0.83
Occipital Lobe3.77 ± 0.84
Parietal Lobe2.5 ± 0.64
Pontine Tegmentum2.47 ± 0.72
Striatum2.47 ± 0.75
Subthalamus2.45 ± 0.89
Temporal Lobe2.53 ± 0.81
Thalamus2.11 ± 0.7
White Matter2.7 ± 0.26
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Scn5aCBCerebellum15.48
23.42
Scn5aCTXCerebral cortex5.41
4.24
Scn5aHIPHippocampal region4.89
4.59
Scn5aHPFHippocampal formation6.99
6.26
Scn5aHYHypothalamus6.22
4.57
Scn5aLSXLateral septal complex52.57
38.58
Scn5aMBMidbrain3
3.06
Scn5aMYMedulla5.77
6.7
Scn5aOLFOlfactory bulb21.75
17.12
Scn5aPPons4.69
4.86
Scn5aPALPallidum17.4
14.19
Scn5aRHPRetrohippocampal region9.78
8.02
Scn5asAMYStriatum-like amygdalar nuclei50.16
38.08
Scn5aSTRStriatum12.88
9.68
Scn5aSTRdStriatum dorsal region4.72
3.49
Scn5aSTRvStriatum ventral region7.89
6.69
Scn5aTHThalamus6.07
5.39
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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