AutismKB 2.0

Annotation Detail for VPS39


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Basic Information Top
Gene Symbol:VPS39 ( FLJ21681,FLJ46546,KIAA0770,TLP,VAM6,hVam6p )
Gene Full Name: vacuolar protein sorting 39 homolog (S. cerevisiae)
Band: 15q15.1
Quick LinksEntrez ID:23339; OMIM: 612188; Uniprot ID:VPS39_HUMAN; ENSEMBL ID: ENSG00000166887; HGNC ID: 20593
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 body7 / 7076198
blastocyst5 / 6231980
fetus26 / 56401246
neonate0 / 310970 
infant3 / 23620127
juvenile3 / 5555653
adult155 / 193912179
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adrenal tumor1 / 1279478
bladder carcinoma7 / 17475400
breast (mammary gland) tumor7 / 9417874
cervical tumor5 / 34366145
chondrosarcoma9 / 82823108
colorectal tumor6 / 11424652
esophageal tumor1 / 1729057
gastrointestinal tumor10 / 11936983
germ cell tumor10 / 26384537
glioma8 / 10688374
head and neck tumor10 / 13630273
kidney tumor10 / 68959145
leukemia10 / 95842104
liver tumor3 / 9635931
lung tumor5 / 10312748
lymphoma2 / 7175527
non-neoplasia2 / 9725020
normal223 / 336030766
ovarian tumor1 / 7668213
pancreatic tumor12 / 104616114
primitive neuroectodermal tumor of the CNS9 / 12568071
prostate cancer3 / 10268029
retinoblastoma1 / 4635621
skin tumor6 / 12494948
soft tissue/muscle tissue tumor13 / 125191103
uterine tumor7 / 9025777
Pool Name Gene EST/Total EST in pool Transcripts per million(TPM) Bar based on TPM
adipose tissue0 / 131060 
adrenal gland2 / 3319760
ascites6 / 40015149
bladder8 / 29757268
blood10 / 12347880
bone6 / 7165583
bone marrow1 / 4880120
brain63 / 110098957
cervix6 / 48171124
connective tissue14 / 14925593
ear0 / 162120 
embryonic tissue14 / 21572264
esophagus1 / 2020949
eye7 / 21105433
heart2 / 8962622
intestine11 / 23447246
kidney15 / 21177770
larynx2 / 2414582
liver5 / 20774324
lung17 / 33697450
lymph2 / 4427045
lymph node20 / 91610218
mammary gland10 / 15327165
mouth3 / 6705244
muscle5 / 10771546
nerve1 / 1576863
ovary1 / 1020519
pancreas16 / 21481274
parathyroid2 / 2053997
pharynx2 / 4132848
pituitary gland1 / 1658560
placenta19 / 28082567
prostate9 / 18934547
salivary gland0 / 201550 
skin13 / 21057461
spleen7 / 53952129
stomach6 / 9661962
testis24 / 33044272
thymus11 / 81131135
thyroid4 / 4747384
tonsil4 / 16999235
trachea0 / 524130 
umbilical cord2 / 13680146
uterus24 / 232878103
vascular0 / 517800 
Microarray in BioGPS Top
Select probe  
  • Microarray Platform: GeneAtlas U133A, gcrma
  • Affymatrix Probe ID: 212156_at
Cell line Expression level Expression bar
721_B_lymphoblasts174.3
Adipocyte75.4
AdrenalCortex55.2
Adrenalgland78.2
Amygdala120.55
Appendix31.3
AtrioventricularNode22.2
BDCA4+_DentriticCells170.25
Bonemarrow56.65
BronchialEpithelialCells32.1
CD105+_Endothelial20.3
CD14+_Monocytes70.4
CD19+_BCells(neg._sel.)75.1
CD33+_Myeloid49.05
CD34+54.4
CD4+_Tcells352.2
CD56+_NKCells170.55
CD71+_EarlyErythroid32.3
CD8+_Tcells239.15
CardiacMyocytes145.05
Caudatenucleus92.8
Cerebellum113.85
CerebellumPeduncles148.85
CiliaryGanglion23.95
CingulateCortex122.65
Colorectaladenocarcinoma77.25
DorsalRootGanglion28.25
FetalThyroid89
Fetalbrain92.2
Fetalliver35.6
Fetallung72.3
GlobusPallidus53.9
Heart71.8
Hypothalamus98.6
Kidney77.65
Leukemia_chronicMyelogenousK-56262.45
Leukemia_promyelocytic-HL-6065.3
Leukemialymphoblastic(MOLT-4)78.65
Liver102.75
Lung54.8
Lymphnode78.65
Lymphoma_burkitts(Daudi)105.7
Lymphoma_burkitts(Raji)122.25
MedullaOblongata70.6
OccipitalLobe90.4
OlfactoryBulb38.05
Ovary57.7
Pancreas75.2
PancreaticIslet68.55
ParietalLobe73.4
Pituitary94
Placenta90.35
Pons98.65
PrefrontalCortex193.35
Prostate93.25
Salivarygland71.15
SkeletalMuscle32.9
Skin21.95
SmoothMuscle119.25
Spinalcord86.6
SubthalamicNucleus52.05
SuperiorCervicalGanglion22.35
TemporalLobe71.25
Testis76.85
TestisGermCell73.8
TestisIntersitial50.05
TestisLeydigCell93.15
TestisSeminiferousTubule100.7
Thalamus89.45
Thymus72.75
Thyroid164.9
Tongue77.9
Tonsil73.6
Trachea75.55
TrigeminalGanglion33.95
Uterus61.1
UterusCorpus21.75
WholeBlood132
Wholebrain99.5
colon71.1
pineal_day133.18
pineal_night93.4
retina116.8
small_intestine51.5
Allen Brain Atlas Top
Human Whole Brain Microarrayview in Allen Brain Atlas
  • Probe id     Donor id      
  • Probe name: A_23_P100103
  • 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
Amygdala7.25 ± 0.3
Basal Forebrain7.24 ± 0.15
Basal Part of Pons7.05 ± 0.4
Cerebellar Cortex6.96 ± 0.38
Cerebellar Nuclei7.37 ± 0.29
Claustrum7.58 ± 0.61
Epithalamus7.22 ± 0.35
Frontal Lobe7.11 ± 0.4
Globus Pallidus7.34 ± 0.23
Hypothalamus7.27 ± 0.29
Insula7.05 ± 0.36
Limbic Lobe7.51 ± 0.42
Mesencephalon7.32 ± 0.32
Myelencephalon7.28 ± 0.33
Occipital Lobe7.7 ± 0.31
Parietal Lobe7.35 ± 0.39
Pontine Tegmentum7.3 ± 0.47
Striatum7.58 ± 0.42
Subthalamus7 ± 0.29
Temporal Lobe7.2 ± 0.34
Thalamus7.17 ± 0.28
White Matter7.32 ± 0.52
Mouse Brain ISH
Gene Symbol Brain Structure ID Brain Structure Name Express Desity/Level (Meatured by ISH) Express Bar
Vps39CBCerebellum7.45
8.82
Vps39CTXCerebral cortex22.96
18.63
Vps39HIPHippocampal region25.29
35.58
Vps39HPFHippocampal formation23.75
27.59
Vps39HYHypothalamus18.45
17.06
Vps39LSXLateral septal complex4.39
3.25
Vps39MBMidbrain14.39
17.4
Vps39MYMedulla15.53
21.86
Vps39OLFOlfactory bulb20.2
17.68
Vps39PPons17.34
22.36
Vps39PALPallidum16.1
17.69
Vps39RHPRetrohippocampal region22.52
20.11
Vps39sAMYStriatum-like amygdalar nuclei16.78
13.7
Vps39STRStriatum7.99
6.77
Vps39STRdStriatum dorsal region6.58
5.62
Vps39STRvStriatum ventral region9.07
7.72
Vps39THThalamus15.23
14.82
Peptide Top
Peptide Name Peptide Lengh Peptide Start Peptide End Peptide Sequence Source
PAp00039610 25 228 252 CALNWTDIPVAMEHQPPYIIAVLPR 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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