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mutLBSgeneDB |
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| Gene summary for PDCD10 |
 Gene summary |
| Basic gene Info. | Gene symbol | PDCD10 |
| Gene name | programmed cell death 10 | |
| Synonyms | CCM3|TFAR15 | |
| Cytomap | UCSC genome browser: 3q26.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_007217.3, NM_145859.1,NM_145860.1, | |
| Description | TF-1 cell apoptosis-related protein 15apoptosis-related protein 15cerebral cavernous malformations 3 proteinprogrammed cell death protein 10 | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 609118 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000114209 | ||
| HPRD : 10141 | ||
| Vega : OTTHUMG00000158415 | ||
| Protein | UniProt: Q9BUL8 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PDCD10 | |
| BioGPS: 11235 | ||
| Pathway | NCI Pathway Interaction Database: PDCD10 | |
| KEGG: PDCD10 | ||
| REACTOME: PDCD10 | ||
| Pathway Commons: PDCD10 | ||
| Context | iHOP: PDCD10 | |
| ligand binding site mutation search in PubMed: PDCD10 | ||
| UCL Cancer Institute: PDCD10 | ||
| 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:0008284 | positive regulation of cell proliferation | 17360971 | GO:0030335 | positive regulation of cell migration | 23541896 | GO:0032874 | positive regulation of stress-activated MAPK cascade | 22652780 | GO:0042542 | response to hydrogen peroxide | 22291017 | GO:0043066 | negative regulation of apoptotic process | 17360971 | GO:0043406 | positive regulation of MAP kinase activity | 17360971 |
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| Ligand binding site mutations for PDCD10 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | K70 | K69N | STAD | 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 PDCD10 |
| 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 | K70 | K69N | -1.156551 |
| (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 PDCD10 from PDB |
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| Differential gene expression and gene-gene network for PDCD10 |
| 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 PDCD10 |
| 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 PDCD10 |
| 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 PDCD10 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | 4IP | INOSITOL 1,3,4,5-TETRAKISPHOSPHATE | 3ajm | A | K70 | 4IP | INOSITOL 1,3,4,5-TETRAKISPHOSPHATE | 3ajm | B | K70 |
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| Conservation information for LBS of PDCD10 |
| Multiple alignments for Q9BUL8 in multiple species |
| LBS | AA sequence | # species | Species | A135 | TIKDIASAIKE | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | A135 | TIKLIASSIKK | 1 | Caenorhabditis elegans | F182 | TLKTYFKDGKA | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | F182 | TLKTYFKDQNA | 1 | Caenorhabditis elegans | G185 | TYFKDGKAINV | 5 | Homo sapiens, Danio rerio, Rattus norvegicus, Gallus gallus, Mus musculus | G185 | TYFKDQNANQV | 1 | Caenorhabditis elegans | G185 | TYFKDGKALNV | 1 | Xenopus tropicalis | I131 | RFLQTIKDIAS | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | I131 | AFLETIKLIAS | 1 | Caenorhabditis elegans | I138 | DIASAIKELLD | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | I138 | LIASSIKKLLE | 1 | Caenorhabditis elegans | K132 | FLQTIKDIASA | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | K132 | FLETIKLIASS | 1 | Caenorhabditis elegans | K139 | IASAIKELLDT | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | K139 | IASSIKKLLEA | 1 | Caenorhabditis elegans | K164 | ALEHQKKEFVK | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | K164 | AVEKRKREFVH | 1 | Caenorhabditis elegans | K172 | FVKYSKSFSDT | 5 | Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | K172 | FVHYSKRFSNT | 1 | Caenorhabditis elegans | K172 | FVKHSKSFSDT | 1 | Danio rerio | K179 | FSDTLKTYFKD | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | K179 | FSNTLKTYFKD | 1 | Caenorhabditis elegans | K186 | YFKDGKAINVF | 5 | Homo sapiens, Danio rerio, Rattus norvegicus, Gallus gallus, Mus musculus | K186 | YFKDQNANQVS | 1 | Caenorhabditis elegans | K186 | YFKDGKALNVF | 1 | Xenopus tropicalis | K70 | KILEKKSVEVN | 4 | Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Mus musculus | K70 | VLLDDSELSVN | 1 | Caenorhabditis elegans | K70 | KILEKKNVEIN | 1 | Danio rerio | K70 | KILEKKSVDVN | 1 | Gallus gallus | L128 | DRVRFLQTIKD | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | L128 | DRHAFLETIKL | 1 | Caenorhabditis elegans | L142 | AIKELLDTVNN | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | L142 | SIKKLLEAINA | 1 | Caenorhabditis elegans | N146 | LLDTVNNVFKK | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | N146 | LLEAINAVYRI | 1 | Caenorhabditis elegans | S171 | EFVKYSKSFSD | 5 | Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | S171 | EFVHYSKRFSN | 1 | Caenorhabditis elegans | S171 | EFVKHSKSFSD | 1 | Danio rerio | S175 | YSKSFSDTLKT | 5 | Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | S175 | YSKRFSNTLKT | 1 | Caenorhabditis elegans | S175 | HSKSFSDTLKT | 1 | Danio rerio | V168 | QKKEFVKYSKS | 5 | Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Gallus gallus, Mus musculus | V168 | RKREFVHYSKR | 1 | Caenorhabditis elegans | V168 | QKKEFVKHSKS | 1 | Danio rerio |
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