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mutLBSgeneDB |
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| Gene summary for CAPN3 |
 Gene summary |
| Basic gene Info. | Gene symbol | CAPN3 |
| Gene name | calpain 3, (p94) | |
| Synonyms | CANP3|CANPL3|LGMD2|LGMD2A|nCL-1|p94 | |
| Cytomap | UCSC genome browser: 15q15.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000070.2, NM_024344.1,NM_173087.1,NM_173088.1,NM_173089.1, NM_173090.1,NM_212465.2,NR_027911.1,NR_027912.1, | |
| Description | calpain p94, large [catalytic] subunitcalpain, large polypeptide L3calpain-3muscle-specific calcium-activated neutral protease 3 large subunitnew calpain 1 | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 114240 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000092529 | ||
| HPRD : 00255 | ||
| Vega : OTTHUMG00000130619 | ||
| Protein | UniProt: P20807 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_CAPN3 | |
| BioGPS: 825 | ||
| Pathway | NCI Pathway Interaction Database: CAPN3 | |
| KEGG: CAPN3 | ||
| REACTOME: CAPN3 | ||
| Pathway Commons: CAPN3 | ||
| Context | iHOP: CAPN3 | |
| ligand binding site mutation search in PubMed: CAPN3 | ||
| UCL Cancer Institute: CAPN3 | ||
| 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:0006508 | proteolysis | 18310072 | GO:0033234 | negative regulation of protein sumoylation | 20694146 | GO:0050790 | regulation of catalytic activity | 20694146 | GO:0097264 | self proteolysis | 9642272 |
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| Ligand binding site mutations for CAPN3 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | E672 | D671N | BLCA | 1 | D800 | D800H | HNSC | 1 | E672 | D671E | KIRC | 1 | I742 | I742M | LUAD | 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 CAPN3 |
| 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 | E672 | D671E | 0.39782158 | D800 | D800H | -0.63449491 | I742 | I742M | -0.39420539 | E672 | D671N | -0.096626645 |
| (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 CAPN3 from PDB |
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| Differential gene expression and gene-gene network for CAPN3 |
| 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 CAPN3 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1869123 | Limb-girdle muscular dystrophy type 2A | 54 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for CAPN3 |
| 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 CAPN3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 4okh | A | D800 | CA | CALCIUM(2+) | 4okh | B | D800 | CA | CALCIUM(2+) | 4okh | C | D800 | CA | CALCIUM(2+) | 4okh | A | E672 | CA | CALCIUM(2+) | 4okh | B | E672 | CA | CALCIUM(2+) | 4okh | A | I742 | CA | CALCIUM(2+) | 4okh | C | I742 |
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| Conservation information for LBS of CAPN3 |
| Multiple alignments for P20807 in multiple species |
| LBS | AA sequence | # species | Species | A662 | IFRQIAGDDME | 3 | Bos taurus, Mus musculus, Rattus norvegicus | A662 | IFKQIAGDDME | 1 | Homo sapiens | D665 | QIAGDDMEICA | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D705 | MIALMDTDGSG | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D707 | ALMDTDGSGRL | 3 | Bos taurus, Mus musculus, Rattus norvegicus | D707 | ALMDTDGSGKL | 1 | Homo sapiens | D735 | IFKHYDTDQSG | 2 | Homo sapiens, Bos taurus | D735 | IFKHYDTDHSG | 2 | Mus musculus, Rattus norvegicus | D737 | KHYDTDQSGTI | 2 | Homo sapiens, Bos taurus | D737 | KHYDTDHSGTI | 2 | Mus musculus, Rattus norvegicus | D800 | AFHAFDKDGDG | 2 | Homo sapiens, Rattus norvegicus | D800 | AFNAFDKDGDG | 2 | Bos taurus, Mus musculus | D802 | HAFDKDGDGII | 2 | Homo sapiens, Rattus norvegicus | D802 | NAFDKDGDGII | 2 | Bos taurus, Mus musculus | D804 | FDKDGDGIIKL | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E667 | AGDDMEICADE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E672 | EICADELKNVL | 3 | Bos taurus, Mus musculus, Rattus norvegicus | E672 | EICADELKKVL | 1 | Homo sapiens | E716 | RLNLQEFHHLW | 3 | Bos taurus, Mus musculus, Rattus norvegicus | E716 | KLNLQEFHHLW | 1 | Homo sapiens | I742 | DQSGTINSYEM | 2 | Homo sapiens, Bos taurus | I742 | DHSGTINSYEM | 2 | Mus musculus, Rattus norvegicus | I806 | KDGDGIIKLNV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K711 | TDGSGRLNLQE | 3 | Bos taurus, Mus musculus, Rattus norvegicus | K711 | TDGSGKLNLQE | 1 | Homo sapiens | K808 | GDGIIKLNVLE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | S709 | MDTDGSGRLNL | 3 | Bos taurus, Mus musculus, Rattus norvegicus | S709 | MDTDGSGKLNL | 1 | Homo sapiens | S739 | YDTDQSGTINS | 2 | Homo sapiens, Bos taurus | S739 | YDTDHSGTINS | 2 | Mus musculus, Rattus norvegicus | T741 | TDQSGTINSYE | 2 | Homo sapiens, Bos taurus | T741 | TDHSGTINSYE | 2 | Mus musculus, Rattus norvegicus |
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