mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for NRP1
Gene summary
Basic gene Info.Gene symbolNRP1
Gene nameneuropilin 1
CytomapUCSC genome browser: 10p12
Type of geneprotein-coding
Descriptionneuropilin-1transmembrane receptorvascular endothelial cell growth factor 165 receptor
Modification date20141222
dbXrefs MIM : 602069
Ensembl : ENSG00000099250
HPRD : 03642
Vega : OTTHUMG00000019343
ProteinUniProt: O14786
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NRP1
BioGPS: 8829
PathwayNCI Pathway Interaction Database: NRP1
Pathway Commons: NRP1
ContextiHOP: NRP1
ligand binding site mutation search in PubMed: NRP1
UCL Cancer Institute: NRP1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

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.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

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

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.
LBSAAchange of nsSNVRelative stability change
(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

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)
* Left PPI network was created from samples with mutations in the LBS of NRP1 and the right PPI network was created from samples without mutations in the LBS of NRP1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for NRP1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0030297Pancreatic Neoplasms3AlteredExpression, Biomarker
umls:C0033578Prostatic Neoplasms2Biomarker
umls:C0023895Liver Diseases1Biomarker
umls:C0031117Peripheral Nervous System Diseases1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NRP1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of NRP1
Multiple alignments for O14786 in multiple species
LBSAA sequence# speciesSpecies
A252FYTDSAIAKEG4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D209MFCRYDRLEIW2Homo sapiens, Mus musculus
D209AFCRYDRLEIW1Gallus gallus
D209VFCRYDRLEIW1Rattus norvegicus
D250MVFYTDSAIAK4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D320WTPGEDSYREW2Homo sapiens, Rattus norvegicus
D320WTPGEDSVREW1Gallus gallus
D320WTPGEDSYKEW1Mus musculus
E348GAISKETKKKY3Homo sapiens, Mus musculus, Rattus norvegicus
E348GAISKETKKEY1Gallus gallus
G414ATWETGISMRF1Homo sapiens
G414VSWENGVSLRF1Gallus gallus
G414VSWETGISMRF1Mus musculus
G414ASWETGISMRF1Rattus norvegicus
I253YTDSAIAKEGF4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I415SWETGISMRFE2Mus musculus, Rattus norvegicus
I415TWETGISMRFE1Homo sapiens
I415SWENGVSLRFE1Gallus gallus
N300SQYGTNWSVER2Mus musculus, Rattus norvegicus
N300SQYSTNWSAER1Homo sapiens
N300SQYSAIWSSER1Gallus gallus
S298ASSQYGTNWSV2Mus musculus, Rattus norvegicus
S298ASSQYSTNWSA1Homo sapiens
S298VSSQYSAIWSS1Gallus gallus
S346TQGAISKETKK4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T316PENGWTPGEDS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T349AISKETKKKYY3Homo sapiens, Mus musculus, Rattus norvegicus
T349AISKETKKEYY1Gallus gallus
W301QYGTNWSVERS2Mus musculus, Rattus norvegicus
W301QYSTNWSAERS1Homo sapiens
W301QYSAIWSSERS1Gallus gallus
Y297TASSQYGTNWS2Mus musculus, Rattus norvegicus
Y297TASSQYSTNWS1Homo sapiens
Y297TVSSQYSAIWS1Gallus gallus
Y353ETKKKYYVKTY3Homo sapiens, Mus musculus, Rattus norvegicus
Y353ETKKEYYLKTY1Gallus gallus

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