AutismKB 2.0

Annotation Detail for CLN3


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Basic Information Top
Gene Symbol:CLN3 ( BTS,JNCL,MGC102840 )
Gene Full Name: ceroid-lipofuscinosis, neuronal 3
Band: 16p12.1
Quick LinksEntrez ID:1201; OMIM: 607042; Uniprot ID:CLN3_HUMAN; ENSEMBL ID: ENSG00000188603; HGNC ID: 2074
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 body2 / 7076128
blastocyst2 / 6231932
fetus27 / 56401247
neonate2 / 3109764
infant2 / 2362084
juvenile1 / 5555617
adult249 / 1939121128
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) tumor18 / 94178191
cervical tumor4 / 34366116
chondrosarcoma6 / 8282372
colorectal tumor12 / 114246105
esophageal tumor2 / 17290115
gastrointestinal tumor11 / 11936992
germ cell tumor28 / 263845106
glioma4 / 10688337
head and neck tumor1 / 1363027
kidney tumor2 / 6895929
leukemia6 / 9584262
liver tumor8 / 9635983
lung tumor10 / 10312796
lymphoma5 / 7175569
non-neoplasia9 / 9725092
normal325 / 336030796
ovarian tumor8 / 76682104
pancreatic tumor7 / 10461666
primitive neuroectodermal tumor of the CNS28 / 125680222
prostate cancer11 / 102680107
retinoblastoma0 / 463560 
skin tumor8 / 12494964
soft tissue/muscle tissue tumor10 / 12519179
uterine tumor4 / 9025744
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland3 / 3319790
ascites5 / 40015124
bladder1 / 2975733
blood14 / 123478113
bone7 / 7165597
bone marrow3 / 4880161
brain82 / 110098974
cervix17 / 48171352
connective tissue18 / 149255120
ear0 / 162120 
embryonic tissue8 / 21572237
esophagus3 / 20209148
eye11 / 21105452
heart2 / 8962622
intestine39 / 234472166
kidney34 / 211777160
larynx0 / 241450 
liver9 / 20774343
lung26 / 33697477
lymph1 / 4427022
lymph node4 / 9161043
mammary gland28 / 153271182
mouth0 / 670520 
muscle4 / 10771537
nerve1 / 1576863
ovary13 / 102051127
pancreas8 / 21481237
parathyroid5 / 20539243
pharynx0 / 413280 
pituitary gland1 / 1658560
placenta68 / 280825242
prostate24 / 189345126
salivary gland2 / 2015599
skin12 / 21057456
spleen6 / 53952111
stomach9 / 9661993
testis23 / 33044269
thymus11 / 81131135
thyroid0 / 474730 
tonsil0 / 169990 
trachea1 / 5241319
umbilical cord2 / 13680146
uterus15 / 23287864
vascular1 / 5178019
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 209275_s_at
Cell line Expression level Expression bar
721_B_lymphoblasts12.7
Adipocyte13.5
AdrenalCortex7.15
Adrenalgland11.5
Amygdala6.2
Appendix5.15
AtrioventricularNode4.35
BDCA4+_DentriticCells45.5
Bonemarrow6
BronchialEpithelialCells5.8
CD105+_Endothelial6.55
CD14+_Monocytes26.15
CD19+_BCells(neg._sel.)6.4
CD33+_Myeloid15.3
CD34+9.35
CD4+_Tcells39.55
CD56+_NKCells7.75
CD71+_EarlyErythroid5.35
CD8+_Tcells11.7
CardiacMyocytes7.4
Caudatenucleus5.9
Cerebellum4.75
CerebellumPeduncles6.65
CiliaryGanglion4.05
CingulateCortex6.3
Colorectaladenocarcinoma6.7
DorsalRootGanglion4.45
FetalThyroid7.1
Fetalbrain5.7
Fetalliver5.55
Fetallung12.3
GlobusPallidus4.25
Heart12.95
Hypothalamus7.8
Kidney12.3
Leukemia_chronicMyelogenousK-56214.95
Leukemia_promyelocytic-HL-6010.2
Leukemialymphoblastic(MOLT-4)5.8
Liver8.5
Lung16.6
Lymphnode10.3
Lymphoma_burkitts(Daudi)8.05
Lymphoma_burkitts(Raji)8.6
MedullaOblongata5.45
OccipitalLobe5.55
OlfactoryBulb6
Ovary3.75
Pancreas5.45
PancreaticIslet6.8
ParietalLobe6.9
Pituitary6.5
Placenta68.55
Pons5.5
PrefrontalCortex7.2
Prostate18.1
Salivarygland4.65
SkeletalMuscle10.95
Skin4.4
SmoothMuscle7.75
Spinalcord10.9
SubthalamicNucleus5.25
SuperiorCervicalGanglion6.45
TemporalLobe5.25
Testis5.2
TestisGermCell5.35
TestisIntersitial4.9
TestisLeydigCell5.5
TestisSeminiferousTubule5.05
Thalamus6.8
Thymus12.3
Thyroid14.55
Tongue5.8
Tonsil6.7
Trachea6.45
TrigeminalGanglion5.7
Uterus4.8
UterusCorpus7.85
WholeBlood17.8
Wholebrain5.05
colon8.05
pineal_day6.32
pineal_night5.92
retina12.475
small_intestine6
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: A_24_P179071
  • 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
Amygdala4.66 ± 0.49
Basal Forebrain4.27 ± 0.49
Basal Part of Pons4.23 ± 0.42
Cerebellar Cortex4.82 ± 0.3
Cerebellar Nuclei4.12 ± 0.48
Claustrum4.7 ± 0.51
Epithalamus4.46 ± 0.27
Frontal Lobe4.35 ± 0.52
Globus Pallidus4.73 ± 0.43
Hypothalamus4.32 ± 0.47
Insula4.25 ± 0.35
Limbic Lobe4.55 ± 0.57
Mesencephalon4.41 ± 0.56
Myelencephalon4.44 ± 0.47
Occipital Lobe4.33 ± 0.46
Parietal Lobe4.4 ± 0.59
Pontine Tegmentum4.37 ± 0.56
Striatum4.26 ± 0.48
Subthalamus4.2 ± 0.38
Temporal Lobe4.42 ± 0.42
Thalamus4.3 ± 0.46
White Matter5.47 ± 0.18
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Cln3CBCerebellum3.2
3.25
Cln3CTXCerebral cortex0.76
0.65
Cln3HIPHippocampal region2.1
1.81
Cln3HPFHippocampal formation2.13
1.81
Cln3HYHypothalamus2.34
4.22
Cln3LSXLateral septal complex0.51
0.43
Cln3MBMidbrain0.71
1.34
Cln3MYMedulla2.13
3.17
Cln3OLFOlfactory bulb6.95
6.02
Cln3PPons3.47
5.07
Cln3PALPallidum0.65
1.45
Cln3RHPRetrohippocampal region2.16
1.58
Cln3sAMYStriatum-like amygdalar nuclei0.18
0.12
Cln3STRStriatum0.34
0.28
Cln3STRdStriatum dorsal region0.3
0.26
Cln3STRvStriatum ventral region0.48
0.37
Cln3THThalamus0.46
0.4
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00095830 23 90 112 FDCNSVSTAAVLLADILPTLVIK 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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