mutLBSgeneDB |
Gene summary for CALCOCO2 |
Gene summary |
Basic gene Info. | Gene symbol | CALCOCO2 |
Gene name | calcium binding and coiled-coil domain 2 | |
Synonyms | NDP52 | |
Cytomap | UCSC genome browser: 17q21.32 | |
Type of gene | protein-coding | |
RefGenes | NM_001261390.1, NM_001261391.1,NM_001261393.1,NM_001261395.1,NM_005831.4, | |
Description | antigen nuclear dot 52 kDa proteincalcium-binding and coiled-coil domain-containing protein 2nuclear domain 10 protein 52nuclear domain 10 protein NDP52nuclear dot protein 52 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604587 | |
HGNC : HGNC | ||
Ensembl : ENSG00000136436 | ||
HPRD : 06846 | ||
Vega : OTTHUMG00000160505 | ||
Protein | UniProt: Q13137 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CALCOCO2 | |
BioGPS: 10241 | ||
Pathway | NCI Pathway Interaction Database: CALCOCO2 | |
KEGG: CALCOCO2 | ||
REACTOME: CALCOCO2 | ||
Pathway Commons: CALCOCO2 | ||
Context | iHOP: CALCOCO2 | |
ligand binding site mutation search in PubMed: CALCOCO2 | ||
UCL Cancer Institute: CALCOCO2 | ||
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:0034341 | response to interferon-gamma | 9230084 |
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Ligand binding site mutations for CALCOCO2 |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | C422 | N421S | 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 CALCOCO2 |
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 |
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 | C422 | N421S | -1.010659 |
(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 CALCOCO2 from PDB |
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Differential gene expression and gene-gene network for CALCOCO2 |
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 CALCOCO2 |
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 CALCOCO2 |
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. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of CALCOCO2 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 4xkl | B | C422 | ZN | ZINC(2+) | 4xkl | D | C422 |
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Conservation information for LBS of CALCOCO2 |
Multiple alignments for Q13137 in multiple species |
LBS | AA sequence | # species | Species | C422 | PLCFNCPICDK | 1 | Homo sapiens | C422 | HVQMQCPECGS | 1 | Xenopus tropicalis | C422 | TLSLNCPICDK | 1 | Bos taurus | C425 | FNCPICDKIFP | 1 | Homo sapiens | C425 | MQCPECGSEF- | 1 | Xenopus tropicalis | C425 | LNCPICDKTFP | 1 | Bos taurus | H440 | QIFEDHVFCHS | 1 | Homo sapiens | H440 | QVFQDHIFCHD | 1 | Xenopus tropicalis | H440 | QIFEDHVFCHT | 1 | Bos taurus | H444 | DHVFCHSL--- | 1 | Homo sapiens | H444 | DHIFCHDLEST | 1 | Xenopus tropicalis | H444 | DHVFCHTL--- | 1 | Bos taurus |
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