Gene Page: KDM3B

Summary ?
GeneID51780
SymbolKDM3B
Synonyms5qNCA|C5orf7|JMJD1B|NET22
Descriptionlysine demethylase 3B
ReferenceMIM:609373|HGNC:HGNC:1337|Ensembl:ENSG00000120733|HPRD:11055|Vega:OTTHUMG00000163469
Gene typeprotein-coding
Map location5q31
Pascal p-value3.156E-6
Sherlock p-value0.226
Fetal beta0.387
eGeneAnterior cingulate cortex BA24
SupportAscano FMRP targets
Chromatin Remodeling Genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGC128Genome-wide Association StudyA multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Guipponi_2014Whole Exome Sequencing analysis49 DNMs were identified by comparing the exome of 53 individuals with sporadic SCZ and of their non-affected parents

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP IDChromosomePositionAllelePFunctionGeneUp/Down Distance
rs10043984chr5137712121TC2.176E-8intronicKDM3B

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
KDM3BCTNM_016604p.R1406Wmissense01SchizophreniaDNM:Guipponi_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs1458271255137929950KDM3BENSG00000120733.93.23008E-60.03241665gtex_brain_ba24

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005506iron ion bindingIEA-
GO:0008270zinc ion bindingIEA-
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygenIEA-
GO:0016491oxidoreductase activityIEA-
GO:0046872metal ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0016568chromatin modificationIEA-
GO:0055114oxidation reductionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN 805505All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
AMUNDSON GENOTOXIC SIGNATURE 10568All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514330All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT AND CANCER BOX1 UP 1510All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP 424268All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
CHEOK RESPONSE TO MERCAPTOPURINE AND HD MTX DN 2518All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP 207143All SZGR 2.0 genes in this pathway