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mutLBSgeneDB |
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| Gene summary for KDM4C |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM4C |
| Gene name | lysine (K)-specific demethylase 4C | |
| Synonyms | GASC1|JHDM3C|JMJD2C|TDRD14C|bA146B14.1 | |
| Cytomap | UCSC genome browser: 9p24.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001146694.1, NM_001146695.1,NM_001146696.1,NM_015061.3, | |
| Description | GASC-1 proteinJmjC domain-containing histone demethylation protein 3Cgene amplified in squamous cell carcinoma 1 proteinjumonji domain containing 2Cjumonji domain-containing protein 2Clysine-specific demethylase 4Ctudor domain containing 14C | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 605469 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000107077 | ||
| Ensembl : ENSG00000274527 | ||
| HPRD : 12016 | ||
| Vega : OTTHUMG00000019536 | ||
| Vega : OTTHUMG00000187508 | ||
| Protein | UniProt: Q9H3R0 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM4C | |
| BioGPS: 23081 | ||
| Pathway | NCI Pathway Interaction Database: KDM4C | |
| KEGG: KDM4C | ||
| REACTOME: KDM4C | ||
| Pathway Commons: KDM4C | ||
| Context | iHOP: KDM4C | |
| ligand binding site mutation search in PubMed: KDM4C | ||
| UCL Cancer Institute: KDM4C | ||
| 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 | GO:0006357 | regulation of transcription from RNA polymerase II promoter | 17277772 | GO:0033169 | histone H3-K9 demethylation | 18066052 |
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| Ligand binding site mutations for KDM4C |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | H278 | H278L | HNSC | 1 | N282 | G284V | LUAD | 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 KDM4C |
| 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 |
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| 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 | H278 | H278L | 0.49475042 | N282 | G284V | -0.55913014 |
| (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 KDM4C from PDB |
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| Differential gene expression and gene-gene network for KDM4C |
| 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 KDM4C |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0025149 | Medulloblastoma | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for KDM4C |
| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of KDM4C go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | OGA | N-OXALYLGLYCINE | 2xml | A | H278 | OGA | N-OXALYLGLYCINE | 2xml | B | H278 | FE | IRON(3+) | 4xdo | A | H278 | FE | IRON(3+) | 4xdo | B | H278 | FE | IRON(3+) | 4xdp | A | H278 | FE | IRON(3+) | 4xdp | B | H278 | MMK | 2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL) AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4- CARBOXYLIC ACID | 5fjh | A | H278 | MMK | 2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL) AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4- CARBOXYLIC ACID | 5fjh | B | H278 | EM6 | 6-ETHYL-5-METHYL-7-OXIDANYLIDENE-1H- PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE | 5fjk | A | H278 N282 |
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| Conservation information for LBS of KDM4C |
| Multiple alignments for Q9H3R0 in multiple species |
| LBS | AA sequence | # species | Species |
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