mutLBSgeneDB |
Gene summary for KDM5D |
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Basic gene Info. | Gene symbol | KDM5D |
Gene name | lysine (K)-specific demethylase 5D | |
Synonyms | HY|HYA|JARID1D|SMCY | |
Cytomap | UCSC genome browser: Yq11 | |
Type of gene | protein-coding | |
RefGenes | NM_001146705.1, NM_001146706.1,NM_004653.4, | |
Description | H-YJumonji, AT rich interactive domain 1D (RBP2-like)SMC homolog, Y chromosomeSmcy homolog, Y-linkedhistocompatibility Y antigenhistone demethylase JARID1Djumonji/ARID domain-containing protein 1Dlysine-specific demethylase 5Dprotein SmcYselected | |
Modification date | 20141207 | |
dbXrefs | MIM : 426000 | |
HGNC : HGNC | ||
Ensembl : ENSG00000012817 | ||
Ensembl : ENSG00000278871 | ||
Ensembl : ENSG00000280101 | ||
Ensembl : ENSG00000280358 | ||
HPRD : 02464 | ||
Vega : OTTHUMG00000036508 | ||
Protein | UniProt: Q9BY66 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_KDM5D | |
BioGPS: 8284 | ||
Pathway | NCI Pathway Interaction Database: KDM5D | |
KEGG: KDM5D | ||
REACTOME: KDM5D | ||
Pathway Commons: KDM5D | ||
Context | iHOP: KDM5D | |
ligand binding site mutation search in PubMed: KDM5D | ||
UCL Cancer Institute: KDM5D | ||
Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. |
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GO ID | GO Term | PubMed ID | GO:0034720 | histone H3-K4 demethylation | 17320160 |
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Ligand binding site mutations for KDM5D |
![]() We represented ligand binding site mutations only. (You can see big image via clicking.) ![]() |
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LBS | AAchange of nsSNV | Cancer type | # samples | C320 | S321Y | GBM | 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 KDM5D |
![]() Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
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![]() Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
LBS | AAchange of nsSNV | Relative stability change | C320 | S321Y | -0.88998689 |
(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) |
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Differential gene expression and gene-gene network for KDM5D |
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Phenotype information for KDM5D |
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Disease ID | Disease name | # PubMed | Association type |
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Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for KDM5D |
![]() 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 status | DrugBank ID | Name | Type | Drug structure |
Approved|nutraceutical | DB00126 | Vitamin C | Small molecule | ![]() |
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Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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Conservation information for LBS of KDM5D |
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LBS | AA sequence | # species | Species | C317 | IDSYICQVCSR | 2 | Homo sapiens, Pan troglodytes | C317 | MNSYVCRICSR | 1 | Mus musculus | C320 | YICQVCSRGDE | 2 | Homo sapiens, Pan troglodytes | C320 | YVCRICSRGDE | 1 | Mus musculus | C332 | DKLLFCDGCDD | 2 | Homo sapiens, Pan troglodytes | C332 | DKFLLCDGCSD | 1 | Mus musculus | C335 | LFCDGCDDNYH | 2 | Homo sapiens, Pan troglodytes | C335 | LLCDGCSDNYH | 1 | Mus musculus | C343 | NYHIFCLLPPL | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C358 | RGIWRCPKCIL | 2 | Homo sapiens, Pan troglodytes | C358 | KGVWRCPKCIL | 1 | Mus musculus | C361 | WRCPKCILAEC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | H340 | CDDNYHIFCLL | 2 | Homo sapiens, Pan troglodytes | H340 | CSDNYHIFCLL | 1 | Mus musculus |
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