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mutLBSgeneDB |
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| Gene summary for PDCD6 |
 Gene summary |
| Basic gene Info. | Gene symbol | PDCD6 |
| Gene name | programmed cell death 6 | |
| Synonyms | ALG-2|ALG2|PEF1B | |
| Cytomap | UCSC genome browser: 5p15.33 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001267556.1, NM_001267557.1,NM_001267558.1,NM_001267559.1,NM_013232.3, NR_073609.1, | |
| Description | apoptosis-linked gene 2 proteinprobable calcium-binding protein ALG-2programmed cell death protein 6 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601057 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000249915 | ||
| HPRD : 03035 | ||
| Vega : OTTHUMG00000090283 | ||
| Protein | UniProt: O75340 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PDCD6 | |
| BioGPS: 10016 | ||
| Pathway | NCI Pathway Interaction Database: PDCD6 | |
| KEGG: PDCD6 | ||
| REACTOME: PDCD6 | ||
| Pathway Commons: PDCD6 | ||
| Context | iHOP: PDCD6 | |
| ligand binding site mutation search in PubMed: PDCD6 | ||
| UCL Cancer Institute: PDCD6 | ||
| 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:0001938 | positive regulation of endothelial cell proliferation | 21893193 | GO:0006886 | intracellular protein transport | 21122810 | GO:0010595 | positive regulation of endothelial cell migration | 21893193 | GO:0030948 | negative regulation of vascular endothelial growth factor receptor signaling pathway | 21893193 | GO:0032007 | negative regulation of TOR signaling | 21893193 | GO:0034605 | cellular response to heat | 21122810 | GO:0036324 | vascular endothelial growth factor receptor-2 signaling pathway | 21893193 | GO:0043280 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 16132846 | GO:0045766 | positive regulation of angiogenesis | 21893193 | GO:0051898 | negative regulation of protein kinase B signaling | 21893193 |
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| Ligand binding site mutations for PDCD6 |
| 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 | L52 | L52V | BRCA | 1 | E47 | E47K | BRCA | 1 | R166,Y168 | R167H | COAD | 1 | Q145 | R143W | COAD | 1 | G123 | G123S | COAD | 1 | F85 | S83G | 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 PDCD6 |
| 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 | L52 | L52V | -1.4196088 | F85 | S83G | -1.2736289 | Y168 | R167H | -1.2704574 | R166 | R167H | -1.2704574 | E47 | E47K | -0.94070014 | Q145 | R143W | -0.55896353 | G123 | G123S | -0.43781548 |
| (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 PDCD6 from PDB |
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| Differential gene expression and gene-gene network for PDCD6 |
| 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 PDCD6 |
| 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 PDCD6 |
| 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 PDCD6 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2zn8 | A | E47 | CA | CALCIUM(2+) | 2zn9 | A | E47 | CA | CALCIUM(2+) | 2zn9 | B | E47 | ZN | ZINC(2+) | 2zne | A | E47 | ZN | ZINC(2+) | 2zne | B | E47 | CA | CALCIUM(2+) | 2zrs | A | E47 | CA | CALCIUM(2+) | 2zrs | B | E47 | CA | CALCIUM(2+) | 2zrs | C | E47 | CA | CALCIUM(2+) | 2zrs | D | E47 | CA | CALCIUM(2+) | 2zrs | E | E47 | CA | CALCIUM(2+) | 2zrs | F | E47 | CA | CALCIUM(2+) | 2zrs | G | E47 | CA | CALCIUM(2+) | 2zrs | H | E47 | ZN | ZINC(2+) | 2zrt | B | E47 | ZN | ZINC(2+) | 2zrt | C | E47 | ZN | ZINC(2+) | 2zrt | D | E47 | ZN | ZINC(2+) | 2zrt | E | E47 | ZN | ZINC(2+) | 2zrt | F | E47 | ZN | ZINC(2+) | 2zrt | G | E47 | CA | CALCIUM(2+) | 3aaj | A | E47 | CA | CALCIUM(2+) | 3aaj | B | E47 | ZN | ZINC(2+) | 3aak | A | E47 | ZN | ZINC(2+) | 3wxa | A | E47 | ZN | ZINC(2+) | 3wxa | B | E47 | III | Peptide ligand (GLY,PRO,PRO,TYR,PRO,THR,TYR,PRO,GLY,TYR,PRO,GLY,TYR,SER,GLN) | 2zne | A | G123 R166 | III | Peptide ligand (ASN,PRO,PRO,PRO,PRO,GLY,PHE,ILE,MET,HIS,GLY,ASN) | 3wxa | A | L52 F85 | III | Peptide ligand (ASN,PRO,PRO,PRO,PRO,GLY,PHE,ILE,MET,HIS,GLY,ASN) | 3wxa | B | L52 F85 | ZN | ZINC(2+) | 2zn8 | A | Q145 | ZN | ZINC(2+) | 2zrt | B | Q145 | ZN | ZINC(2+) | 2zrt | C | Q145 | ZN | ZINC(2+) | 3wxa | A | Q145 | CA | CALCIUM(2+) | 2zrs | D | Y168 | CA | CALCIUM(2+) | 2zrs | G | Y168 | CA | CALCIUM(2+) | 2zrs | H | Y168 |
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| Conservation information for LBS of PDCD6 |
| Multiple alignments for O75340 in multiple species |
| LBS | AA sequence | # species | Species |
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