mutLBSgeneDB |
Gene summary for KDM6B |
Gene summary |
Basic gene Info. | Gene symbol | KDM6B |
Gene name | lysine (K)-specific demethylase 6B | |
Synonyms | JMJD3 | |
Cytomap | UCSC genome browser: 17p13.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001080424.1, | |
Description | jmjC domain-containing protein 3jumonji domain containing 3, histone lysine demethylasejumonji domain-containing protein 3lysine demethylase 6Blysine-specific demethylase 6B | |
Modification date | 20141207 | |
dbXrefs | MIM : 611577 | |
HGNC : HGNC | ||
Ensembl : ENSG00000132510 | ||
Vega : OTTHUMG00000178021 | ||
Protein | UniProt: O15054 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_KDM6B | |
BioGPS: 23135 | ||
Pathway | NCI Pathway Interaction Database: KDM6B | |
KEGG: KDM6B | ||
REACTOME: KDM6B | ||
Pathway Commons: KDM6B | ||
Context | iHOP: KDM6B | |
ligand binding site mutation search in PubMed: KDM6B | ||
UCL Cancer Institute: KDM6B | ||
Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID |
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Ligand binding site mutations for KDM6B |
Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.) : non-synonymous mutation on LBS, Circle size denotes number of samples. |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | I1464 | V1462M | UCEC | 1 | N1331 | D1333E | UCEC | 1 | C1578 | E1577K | UCEC | 1 | R1246 | R1246H | UCEC | 1 |
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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Protein structure related information for KDM6B |
Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
: nsSNV at non-LBS: nsSNV at LBS |
nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
LBS | AAchange of nsSNV | Relative stability change | I1464 | V1462M | -1.2701325 | R1246 | R1246H | -1.0668153 | N1331 | D1333E | -0.89451022 | C1578 | E1577K | -0.69453538 |
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
Structure image for KDM6B from PDB |
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Differential gene expression and gene-gene network for KDM6B |
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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Phenotype information for KDM6B |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0010606 | Carcinoma, Adenoid Cystic | 1 | Biomarker |
umls:C3714756 | Intellectual Disability | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for KDM6B |
Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of KDM6B go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2xue | A | C1578 | ZN | ZINC(2+) | 2xue | B | C1578 | ZN | ZINC(2+) | 4ask | A | C1578 | ZN | ZINC(2+) | 4ask | B | C1578 | K0I | 3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3- BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC ACID | 3-((6-(4,5-DIHYDRO-1H-BENZO[D]AZEPIN-3(2H)- YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO) PROPANOIC ACID | 4ask | A | R1246 N1331 | K0I | 3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3- BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC ACID | 3-((6-(4,5-DIHYDRO-1H-BENZO[D]AZEPIN-3(2H)- YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO) PROPANOIC ACID | 4ask | B | R1246 N1331 |
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Conservation information for LBS of KDM6B |
Multiple alignments for O15054 in multiple species |
LBS | AA sequence | # species | Species |
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