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mutLBSgeneDB |
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| Gene summary for PRPF4B |
 Gene summary |
| Basic gene Info. | Gene symbol | PRPF4B |
| Gene name | pre-mRNA processing factor 4B | |
| Synonyms | PR4H|PRP4|PRP4H|PRP4K|dJ1013A10.1 | |
| Cytomap | UCSC genome browser: 6p25.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003913.4, NM_176800.2, | |
| Description | PRP4 kinasePRP4 pre-mRNA processing factor 4 homolog BPRP4 pre-mRNA-processing factor 4 homologdJ1013A10.1 (PRP4 protein kinase homolog)protein-serine/threonine kinaseserine/threonine-protein kinase PRP4 homolog | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 602338 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000112739 | ||
| HPRD : 09087 | ||
| Vega : OTTHUMG00000014157 | ||
| Protein | UniProt: Q13523 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PRPF4B | |
| BioGPS: 8899 | ||
| Pathway | NCI Pathway Interaction Database: PRPF4B | |
| KEGG: PRPF4B | ||
| REACTOME: PRPF4B | ||
| Pathway Commons: PRPF4B | ||
| Context | iHOP: PRPF4B | |
| ligand binding site mutation search in PubMed: PRPF4B | ||
| UCL Cancer Institute: PRPF4B | ||
| 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 PRPF4B |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D834 | G836W | LUAD | 1 | D834 | G836V | LUAD | 1 | N773 | N773Y | LUAD | 1 | S771 | S771G | UCEC | 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 PRPF4B |
| 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 | S771 | S771G | -1.2813917 | D834 | G836W | -0.91250774 | D834 | G836V | -0.85480842 | N773 | N773Y | -0.48607622 |
| (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 PRPF4B from PDB |
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| Differential gene expression and gene-gene network for PRPF4B |
| 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 PRPF4B |
| 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 PRPF4B |
| 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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| Gene-centered drug-gene interaction network |
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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 PRPF4B go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ADP | ADP | 4ifc | A | N773 D834 | ADP | ADP | 4ifc | B | N773 D834 | ANP | AMP-PNP | 4iir | A | N773 D834 | ANP | AMP-PNP | 4iir | B | N773 D834 | 1EH | 4-(5-{[(2-CHLOROPYRIDIN-4-YL)METHYL]CARBAMOYL}THIOPHEN- 2-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE | 4ijp | A | S771 | 1EH | 4-(5-{[(2-CHLOROPYRIDIN-4-YL)METHYL]CARBAMOYL}THIOPHEN- 2-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE | 4ijp | B | S771 |
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| Conservation information for LBS of PRPF4B |
| Multiple alignments for Q13523 in multiple species |
| LBS | AA sequence | # species | Species | A715 | ANQEVAVKIIR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D819 | ADIKPDNILVN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D834 | ILKLCDFGSAS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E768 | LCLVFEPLSMN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E776 | SMNLREVLKKY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F698 | TGQGVFSNVVR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F767 | HLCLVFEPLSM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K717 | QEVAVKIIRNN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L751 | DKFHCLRLFRH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L770 | LVFEPLSMNLR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L822 | KPDNILVNESK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M772 | FEPLSMNLREV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N773 | EPLSMNLREVL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N820 | DIKPDNILVNE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R703 | FSNVVRARDNA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S699 | GQGVFSNVVRA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S771 | VFEPLSMNLRE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T693 | NVYGYTGQGVF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V697 | YTGQGVFSNVV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V701 | GVFSNVVRARD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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