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mutLBSgeneDB |
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| Gene summary for HDDC3 |
 Gene summary |
| Basic gene Info. | Gene symbol | HDDC3 |
| Gene name | HD domain containing 3 | |
| Synonyms | (ppGpp)ase|MESH1 | |
| Cytomap | UCSC genome browser: 15q26.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001286451.1, NM_198527.3,NR_104447.1, | |
| Description | HD domain-containing protein 3guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1metazoan SpoT homolog 1penta-phosphate guanosine-3'-pyrophosphohydrolase | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000184508 | ||
| HPRD : 14635 | ||
| Vega : OTTHUMG00000141260 | ||
| Protein | UniProt: Q8N4P3 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HDDC3 | |
| BioGPS: 374659 | ||
| Pathway | NCI Pathway Interaction Database: HDDC3 | |
| KEGG: HDDC3 | ||
| REACTOME: HDDC3 | ||
| Pathway Commons: HDDC3 | ||
| Context | iHOP: HDDC3 | |
| ligand binding site mutation search in PubMed: HDDC3 | ||
| UCL Cancer Institute: HDDC3 | ||
| 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 |
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| Ligand binding site mutations for HDDC3 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D122 | D122G | COAD | 1 | D122 | D122H | OV | 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 HDDC3 |
| 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 | D122 | D122G | -1.1957034 | D122 | D122H | -0.96020153 |
| (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 HDDC3 from PDB |
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| Differential gene expression and gene-gene network for HDDC3 |
| 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 HDDC3 |
| 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 HDDC3 |
| 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 HDDC3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | MN | MANGANESE(2+) | 3nr1 | A | D122 | MN | MANGANESE(2+) | 3nr1 | B | D122 |
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| Conservation information for LBS of HDDC3 |
| Multiple alignments for Q8N4P3 in multiple species |
| LBS | AA sequence | # species | Species | D122 | LVKLADKLYNL | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | D122 | LIKLADKLDNL | 1 | Drosophila melanogaster | D62 | AALLHDTVEDT | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | D62 | AALLHDVVEDT | 1 | Drosophila melanogaster | H35 | TPYINHPIGVA | 3 | Homo sapiens, Danio rerio, Mus musculus | H35 | TPYVNHVINVS | 1 | Drosophila melanogaster | H35 | TPYINHPLGVA | 1 | Xenopus tropicalis | H61 | QAALLHDTVED | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | H61 | MAALLHDVVED | 1 | Drosophila melanogaster |
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