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mutLBSgeneDB |
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| Gene summary for NRP1 |
 Gene summary |
| Basic gene Info. | Gene symbol | NRP1 |
| Gene name | neuropilin 1 | |
| Synonyms | BDCA4|CD304|NP1|NRP|VEGF165R | |
| Cytomap | UCSC genome browser: 10p12 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001024628.2, NM_001024629.2,NM_001244972.1,NM_001244973.1,NM_003873.5, NR_045259.1, | |
| Description | neuropilin-1transmembrane receptorvascular endothelial cell growth factor 165 receptor | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 602069 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000099250 | ||
| HPRD : 03642 | ||
| Vega : OTTHUMG00000019343 | ||
| Protein | UniProt: O14786 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NRP1 | |
| BioGPS: 8829 | ||
| Pathway | NCI Pathway Interaction Database: NRP1 | |
| KEGG: NRP1 | ||
| REACTOME: NRP1 | ||
| Pathway Commons: NRP1 | ||
| Context | iHOP: NRP1 | |
| ligand binding site mutation search in PubMed: NRP1 | ||
| UCL Cancer Institute: NRP1 | ||
| 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 NRP1 |
| 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 | S346 | A344V | SKCM | 1 | D320 | S321F | SKCM | 1 | S346 | A344T | 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 NRP1 |
| 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 | S346 | A344T | -0.56366838 | D320 | S321F | -0.51239795 | S346 | A344V | -0.25515283 |
| (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 NRP1 from PDB |
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| Differential gene expression and gene-gene network for NRP1 |
| 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 NRP1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0030297 | Pancreatic Neoplasms | 3 | AlteredExpression, Biomarker |
| umls:C0033578 | Prostatic Neoplasms | 2 | Biomarker |
| umls:C0014175 | Endometriosis | 1 | Biomarker |
| umls:C0023895 | Liver Diseases | 1 | Biomarker |
| umls:C0031117 | Peripheral Nervous System Diseases | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for NRP1 |
| 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 |
| Approved | DB00039 | Palifermin | Biotech |  |
| Approved|investigational | DB04895 | Pegaptanib | Biotech |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of NRP1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ACT | ACETATE | 4rn5 | A | S346 |
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| Conservation information for LBS of NRP1 |
| Multiple alignments for O14786 in multiple species |
| LBS | AA sequence | # species | Species | A252 | FYTDSAIAKEG | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | D209 | MFCRYDRLEIW | 2 | Homo sapiens, Mus musculus | D209 | AFCRYDRLEIW | 1 | Gallus gallus | D209 | VFCRYDRLEIW | 1 | Rattus norvegicus | D250 | MVFYTDSAIAK | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | D320 | WTPGEDSYREW | 2 | Homo sapiens, Rattus norvegicus | D320 | WTPGEDSVREW | 1 | Gallus gallus | D320 | WTPGEDSYKEW | 1 | Mus musculus | E348 | GAISKETKKKY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E348 | GAISKETKKEY | 1 | Gallus gallus | G414 | ATWETGISMRF | 1 | Homo sapiens | G414 | VSWENGVSLRF | 1 | Gallus gallus | G414 | VSWETGISMRF | 1 | Mus musculus | G414 | ASWETGISMRF | 1 | Rattus norvegicus | I253 | YTDSAIAKEGF | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | I415 | SWETGISMRFE | 2 | Mus musculus, Rattus norvegicus | I415 | TWETGISMRFE | 1 | Homo sapiens | I415 | SWENGVSLRFE | 1 | Gallus gallus | N300 | SQYGTNWSVER | 2 | Mus musculus, Rattus norvegicus | N300 | SQYSTNWSAER | 1 | Homo sapiens | N300 | SQYSAIWSSER | 1 | Gallus gallus | S298 | ASSQYGTNWSV | 2 | Mus musculus, Rattus norvegicus | S298 | ASSQYSTNWSA | 1 | Homo sapiens | S298 | VSSQYSAIWSS | 1 | Gallus gallus | S346 | TQGAISKETKK | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | T316 | PENGWTPGEDS | 4 | Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus | T349 | AISKETKKKYY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T349 | AISKETKKEYY | 1 | Gallus gallus | W301 | QYGTNWSVERS | 2 | Mus musculus, Rattus norvegicus | W301 | QYSTNWSAERS | 1 | Homo sapiens | W301 | QYSAIWSSERS | 1 | Gallus gallus | Y297 | TASSQYGTNWS | 2 | Mus musculus, Rattus norvegicus | Y297 | TASSQYSTNWS | 1 | Homo sapiens | Y297 | TVSSQYSAIWS | 1 | Gallus gallus | Y353 | ETKKKYYVKTY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y353 | ETKKEYYLKTY | 1 | Gallus gallus |
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