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 RPRD1A
Gene summary
Basic gene Info.Gene symbolRPRD1A
Gene nameregulation of nuclear pre-mRNA domain containing 1A
CytomapUCSC genome browser: 18q12.2
Type of geneprotein-coding
DescriptionCyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)cyclin-dependent kinase 2B-inhibitor-related proteinp15INK4B-related proteinregulation of nuclear pre-mRNA domain-containing protein 1A
Modification date20141207
dbXrefs MIM : 610347
Ensembl : ENSG00000141425
HPRD : 10134
Vega : OTTHUMG00000132591
ProteinUniProt: Q96P16
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPRD1A
BioGPS: 55197
PathwayNCI Pathway Interaction Database: RPRD1A
Pathway Commons: RPRD1A
ContextiHOP: RPRD1A
ligand binding site mutation search in PubMed: RPRD1A
UCL Cancer Institute: RPRD1A
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 RPRD1A

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 RPRD1A
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 RPRD1A from PDB

Differential gene expression and gene-gene network for RPRD1A
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 RPRD1A and the right PPI network was created from samples without mutations in the LBS of RPRD1A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for RPRD1A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

Pharmacological information for RPRD1A
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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RPRD1A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of RPRD1A
Multiple alignments for Q96P16 in multiple species
LBSAA sequence# speciesSpecies
D65LYLANDVIQNS4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
D65LYVANDVSQNA1Caenorhabditis elegans
I110GRVLSIWEERS4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
I110GKLINVWKDRQ1Caenorhabditis elegans
N18LSELSNSQQSV4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
N18LTNLSNHPSSI1Caenorhabditis elegans
N64FLYLANDVIQN4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
N64LLYVANDVSQN1Caenorhabditis elegans
Q20ELSNSQQSVQT4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Q20NLSNHPSSIQT1Caenorhabditis elegans
Q68ANDVIQNSKRK4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Q68ANDVSQNARKT1Caenorhabditis elegans
R106KKHLGRVLSIW3Homo sapiens, Bos taurus, Mus musculus
R106EHAIGKLINVW1Caenorhabditis elegans
R106KKHPGRVLSIW1Gallus gallus
R114SIWEERSVYEN4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
R114NVWKDRQIFTP1Caenorhabditis elegans
S19SELSNSQQSVQ4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
S19TNLSNHPSSIQ1Caenorhabditis elegans
V23NSQQSVQTLSL4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
V23NHPSSIQTTSA1Caenorhabditis elegans
Y61L-TFLYLANDV4Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Y61IVNLLYVANDV1Caenorhabditis elegans

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