AutismKB 2.0

Annotation Detail for NLGN3


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Basic Information Top
Gene Symbol:NLGN3 ( HNL3,KIAA1480 )
Gene Full Name: neuroligin 3
Band: Xq13.1
Quick LinksEntrez ID:54413; OMIM: 300336; Uniprot ID:NLGN3_HUMAN; ENSEMBL ID: ENSG00000196338; HGNC ID: 14289
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 body1 / 7076114
blastocyst0 / 623190 
fetus11 / 56401219
neonate0 / 310970 
infant0 / 236200 
juvenile0 / 555560 
adult35 / 193912118
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
glioma12 / 106883112
head and neck tumor0 / 1363020 
kidney tumor0 / 689590 
leukemia0 / 958420 
liver tumor1 / 9635910
lung tumor0 / 1031270 
lymphoma0 / 717550 
non-neoplasia3 / 9725030
normal56 / 336030716
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 tumor1 / 9025711
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland1 / 3319730
ascites0 / 400150 
bladder0 / 297570 
blood0 / 1234780 
bone0 / 716550 
bone marrow0 / 488010 
brain95 / 110098986
cervix0 / 481710 
connective tissue0 / 1492550 
ear0 / 162120 
embryonic tissue2 / 2157229
esophagus0 / 202090 
eye3 / 21105414
heart0 / 896260 
intestine0 / 2344720 
kidney0 / 2117770 
larynx0 / 241450 
liver1 / 2077434
lung0 / 3369740 
lymph0 / 442700 
lymph node0 / 916100 
mammary gland0 / 1532710 
mouth0 / 670520 
muscle0 / 1077150 
nerve0 / 157680 
ovary0 / 1020510 
pancreas0 / 2148120 
parathyroid0 / 205390 
pharynx0 / 413280 
pituitary gland0 / 165850 
placenta1 / 2808253
prostate2 / 18934510
salivary gland0 / 201550 
skin0 / 2105740 
spleen0 / 539520 
stomach0 / 966190 
testis3 / 3304429
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: 219726_at
Cell line Expression level Expression bar
721_B_lymphoblasts9.65
Adipocyte10.15
AdrenalCortex11.25
Adrenalgland9.05
Amygdala11.15
Appendix15.45
AtrioventricularNode8.1
BDCA4+_DentriticCells11.2
Bonemarrow10.05
BronchialEpithelialCells9.35
CD105+_Endothelial10.6
CD14+_Monocytes9.45
CD19+_BCells(neg._sel.)9.45
CD33+_Myeloid12.9
CD34+13.1
CD4+_Tcells10.7
CD56+_NKCells12.35
CD71+_EarlyErythroid9.55
CD8+_Tcells9.25
CardiacMyocytes13
Caudatenucleus10.15
Cerebellum9.15
CerebellumPeduncles14.4
CiliaryGanglion8.15
CingulateCortex17.25
Colorectaladenocarcinoma9.85
DorsalRootGanglion7.9
FetalThyroid9.85
Fetalbrain11.95
Fetalliver8.85
Fetallung7.4
GlobusPallidus10.55
Heart13.6
Hypothalamus12.4
Kidney8.85
Leukemia_chronicMyelogenousK-5629.05
Leukemia_promyelocytic-HL-609.05
Leukemialymphoblastic(MOLT-4)8.35
Liver13.2
Lung9.5
Lymphnode8.95
Lymphoma_burkitts(Daudi)13.15
Lymphoma_burkitts(Raji)14.2
MedullaOblongata10.4
OccipitalLobe13.05
OlfactoryBulb10.6
Ovary6.9
Pancreas9
PancreaticIslet11
ParietalLobe14.9
Pituitary12.05
Placenta10.1
Pons17.4
PrefrontalCortex14.25
Prostate9.7
Salivarygland8.3
SkeletalMuscle17.8
Skin10.2
SmoothMuscle11.3
Spinalcord18.5
SubthalamicNucleus13
SuperiorCervicalGanglion13.35
TemporalLobe15.05
Testis8.65
TestisGermCell8.9
TestisIntersitial8.4
TestisLeydigCell10.3
TestisSeminiferousTubule12.65
Thalamus23.8
Thymus6.15
Thyroid8.55
Tongue9.9
Tonsil9.85
Trachea8.65
TrigeminalGanglion15.75
Uterus7.3
UterusCorpus9.35
WholeBlood10.95
Wholebrain9
colon8.35
pineal_day19.28
pineal_night13.6
retina13.45
small_intestine7.65
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: CUST_10480_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
Amygdala6.11 ± 0.25
Basal Forebrain5.89 ± 0.3
Basal Part of Pons5.74 ± 0.4
Cerebellar Cortex5.51 ± 0.31
Cerebellar Nuclei5.63 ± 0.38
Claustrum5.98 ± 0.6
Epithalamus5.35 ± 0.21
Frontal Lobe5.72 ± 0.32
Globus Pallidus6.06 ± 0.36
Hypothalamus5.43 ± 0.47
Insula5.83 ± 0.28
Limbic Lobe6.04 ± 0.33
Mesencephalon5.67 ± 0.47
Myelencephalon5.82 ± 0.46
Occipital Lobe5.9 ± 0.42
Parietal Lobe5.78 ± 0.47
Pontine Tegmentum5.78 ± 0.41
Striatum6.08 ± 0.33
Subthalamus5.07 ± 0.62
Temporal Lobe5.79 ± 0.38
Thalamus5.86 ± 0.41
White Matter6.51 ± 0.22
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Nlgn3CBCerebellum59.68
100
Nlgn3CTXCerebral cortex100
100
Nlgn3HIPHippocampal region100
100
Nlgn3HPFHippocampal formation100
100
Nlgn3HYHypothalamus100
100
Nlgn3LSXLateral septal complex100
100
Nlgn3MBMidbrain100
100
Nlgn3MYMedulla71.87
84.1
Nlgn3OLFOlfactory bulb100
100
Nlgn3PPons80.43
94.01
Nlgn3PALPallidum100
100
Nlgn3RHPRetrohippocampal region100
100
Nlgn3sAMYStriatum-like amygdalar nuclei100
100
Nlgn3STRStriatum100
100
Nlgn3STRdStriatum dorsal region100
100
Nlgn3STRvStriatum ventral region100
100
Nlgn3THThalamus100
100
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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