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mutLBSgeneDB |
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| Gene summary for KDM4D |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM4D |
| Gene name | lysine (K)-specific demethylase 4D | |
| Synonyms | JMJD2D | |
| Cytomap | UCSC genome browser: 11q21 | |
| Type of gene | protein-coding | |
| RefGenes | NM_018039.2, | |
| Description | jmjC domain-containing histone demethylation protein 3Djumonji domain containing 2Djumonji domain-containing protein 2Dlysine-specific demethylase 4D | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 609766 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000186280 | ||
| HPRD : 17169 | ||
| Vega : OTTHUMG00000167838 | ||
| Protein | UniProt: Q6B0I6 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM4D | |
| BioGPS: 55693 | ||
| Pathway | NCI Pathway Interaction Database: KDM4D | |
| KEGG: KDM4D | ||
| REACTOME: KDM4D | ||
| Pathway Commons: KDM4D | ||
| Context | iHOP: KDM4D | |
| ligand binding site mutation search in PubMed: KDM4D | ||
| UCL Cancer Institute: KDM4D | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0033169 | histone H3-K9 demethylation | 25124442 |
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| Ligand binding site mutations for KDM4D |
| 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 | I259,K255 | N257K | COAD | 1 | A190 | A190V | GBM | 1 | Y89,T87 | Q88R | KIRC | 1 | R316 | R316W | LUAD | 1 | P260 | P260H | LUAD | 1 | C312 | G313V | LUAD | 1 | P232 | P232S | SKCM | 1 | P260 | P260S | SKCM | 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 KDM4D |
| 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 | P260 | P260S | -1.1111553 | P260 | P260H | -1.1039586 | K255 | N257K | -0.88944725 | I259 | N257K | -0.88944725 | P232 | P232S | -0.86007129 | A190 | A190V | -0.80837138 | R316 | R316W | -0.78017746 | C312 | G313V | -0.53003998 | Y89 | Q88R | -0.48188855 | T87 | Q88R | -0.48188855 |
| (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 KDM4D from PDB |
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| Differential gene expression and gene-gene network for KDM4D |
| 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 KDM4D |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for KDM4D |
| 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 KDM4D go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | PDO | PROPANE-1,3-DIOL | 4hon | A | A190 | ZN | ZINC(2+) | 3dxt | A | C312 | ZN | ZINC(2+) | 3dxu | A | C312 | ZN | ZINC(2+) | 4hon | A | C312 | ZN | ZINC(2+) | 4hon | B | C312 | ZN | ZINC(2+) | 4hoo | A | C312 | ZN | ZINC(2+) | 4hoo | B | C312 | ZN | ZINC(2+) | 4d6q | A | C312 | ZN | ZINC(2+) | 4d6r | A | C312 | ZN | ZINC(2+) | 4d6s | A | C312 | ZN | ZINC(2+) | 5f5a | A | C312 | ZN | ZINC(2+) | 5f5c | A | C312 | IEJ | O-TOLUENESULFONAMIDE | 4d6r | A | K255 I259 P260 | PDO | PROPANE-1,3-DIOL | 4hon | A | T87 Y89 P232 | III | Peptide ligand (THR,ALA,ARG,LYS,SER,THR,GLY,GLY,LYS,ALA) | 4hon | A | Y89 R316 | III | Peptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY) | 4hon | B | Y89 R316 |
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| Conservation information for LBS of KDM4D |
| Multiple alignments for Q6B0I6 in multiple species |
| LBS | AA sequence | # species | Species | A138 | SPIYGADVSGS | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | A138 | SPIYGADISGS | 1 | Homo sapiens | A190 | WKTTFAWHTED | 2 | Homo sapiens, Mus musculus | A190 | WKTSFAWHTED | 2 | Rattus norvegicus, Rattus norvegicus | A292 | FNCAEAINFAT | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | C238 | GSSQGCQAFLR | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | C238 | GSSRGCGAFLR | 1 | Homo sapiens | C310 | KVASQCSCGEA | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | C310 | KMASQCSCGEA | 1 | Homo sapiens | C312 | ASQCSCGEARV | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | D139 | PIYGADVSGSL | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | D139 | PIYGADISGSL | 1 | Homo sapiens | E173 | CGIVIEGVNTP | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | E173 | CGVVIEGVNTP | 1 | Homo sapiens | E194 | FAWHTEDMDLY | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | E56 | VIPPKEWRARQ | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | E56 | IIPPKEWKARE | 1 | Homo sapiens | F189 | MWKTTFAWHTE | 2 | Homo sapiens, Mus musculus | F189 | MWKTSFAWHTE | 2 | Rattus norvegicus, Rattus norvegicus | F231 | LAKELFPGSSQ | 2 | Rattus norvegicus, Rattus norvegicus | F231 | LARELFPGSSR | 1 | Homo sapiens | F231 | LARELFPGSSQ | 1 | Mus musculus | F261 | ENGIPFGRITQ | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | F261 | ENGIPFNRITQ | 1 | Homo sapiens | F28 | PTKEEFNDFDK | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | G142 | GADVSGSLFDG | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | G142 | GADISGSLFDE | 1 | Homo sapiens | G174 | GIVIEGVNTPY | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | G174 | GVVIEGVNTPY | 1 | Homo sapiens | H192 | TTFAWHTEDMD | 2 | Homo sapiens, Mus musculus | H192 | TSFAWHTEDMD | 2 | Rattus norvegicus, Rattus norvegicus | H244 | QAFLRHKVALI | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | H244 | GAFLRHKVALI | 1 | Homo sapiens | H280 | FPYGYHAGFNH | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | H90 | VFTQYHKKKKA | 3 | Homo sapiens, Rattus norvegicus, Rattus norvegicus | H90 | VFTQYHKKKKG | 1 | Mus musculus | I140 | IYGADVSGSLF | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | I140 | IYGADISGSLF | 1 | Homo sapiens | I20 | NCSIMIFRPTK | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | I20 | NCNIMIFHPTK | 1 | Homo sapiens | I259 | LKENGIPFGRI | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | I259 | LKENGIPFNRI | 1 | Homo sapiens | I293 | NCAEAINFATP | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | I69 | DNISNILIATP | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | I69 | DNISEILIATP | 1 | Homo sapiens | K210 | HFGQPKTWYAV | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | K210 | HLGEPKTWYVV | 1 | Homo sapiens | K245 | AFLRHKVALIS | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | K25 | IFRPTKEEFND | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | K25 | IFHPTKEEFND | 1 | Homo sapiens | K255 | SPTVLKENGIP | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | L180 | VNTPYLYFGMW | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | M19 | PNCSIMIFRPT | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | M19 | PNCNIMIFHPT | 1 | Homo sapiens | M306 | IDYGKVASQCS | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | M306 | IDYGKMASQCS | 1 | Homo sapiens | N202 | DLYSINYLHFG | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | N202 | DLYSINYLHLG | 1 | Homo sapiens | N29 | TKEEFNDFDKY | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | N294 | CAEAINFATPR | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | P232 | AKELFPGSSQG | 2 | Rattus norvegicus, Rattus norvegicus | P232 | ARELFPGSSRG | 1 | Homo sapiens | P232 | ARELFPGSSQG | 1 | Mus musculus | P260 | KENGIPFGRIT | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | P260 | KENGIPFNRIT | 1 | Homo sapiens | P54 | AKVIPPKEWRA | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | P54 | AKIIPPKEWKA | 1 | Homo sapiens | Q151 | DGKTQQWNVGH | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | Q151 | DENTKQWNLGH | 1 | Homo sapiens | Q221 | PPEHGRRLELL | 2 | Rattus norvegicus, Rattus norvegicus | Q221 | PPEHGQRLERL | 1 | Homo sapiens | Q221 | PPEHGRRLERL | 1 | Mus musculus | R316 | SCGEARVSFSM | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | R316 | SCGEARVTFSM | 1 | Homo sapiens | S141 | YGADVSGSLFD | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | S141 | YGADISGSLFD | 1 | Homo sapiens | S143 | ADVSGSLFDGK | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | S143 | ADISGSLFDEN | 1 | Homo sapiens | S200 | DMDLYSINYLH | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | T87 | QAGVFTQYHKK | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | T87 | RAGVFTQYHKK | 1 | Homo sapiens | V317 | CGEARVSFSMD | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | V317 | CGEARVTFSMD | 1 | Homo sapiens | W212 | GQPKTWYAVPP | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | W212 | GEPKTWYVVPP | 1 | Homo sapiens | W57 | IPPKEWRARQS | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | W57 | IPPKEWKARET | 1 | Homo sapiens | Y136 | YESPIYGADVS | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | Y136 | YNSPIYGADIS | 1 | Homo sapiens | Y179 | GVNTPYLYFGM | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | Y181 | NTPYLYFGMWK | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | Y277 | MVTFPYGYHAG | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus | Y303 | PRWIDYGKVAS | 3 | Mus musculus, Rattus norvegicus, Rattus norvegicus | Y303 | PRWIDYGKMAS | 1 | Homo sapiens | Y89 | GVFTQYHKKKK | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Rattus norvegicus |
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