mutLBSgeneDB

mutLBSgeneDB
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 symbol	RPRD1A
	Gene name	regulation of nuclear pre-mRNA domain containing 1A
	Synonyms	HsT3101\|P15RS
	Cytomap	UCSC genome browser: 18q12.2
	Type of gene	protein-coding
	RefGenes	NM_018170.3,
	Description	Cyclin-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 date	20141207
dbXrefs	MIM : 610347
	HGNC : HGNC
	Ensembl : ENSG00000141425
	HPRD : 10134
	Vega : OTTHUMG00000132591
Protein	UniProt: Q96P16 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RPRD1A
	BioGPS: 55197
Pathway	NCI Pathway Interaction Database: RPRD1A
	KEGG: RPRD1A
	REACTOME: RPRD1A
	Pathway Commons: RPRD1A
Context	iHOP: RPRD1A
	ligand binding site mutation search in PubMed: RPRD1A
	UCL Cancer Institute: RPRD1A
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 RPRD1A

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
S19	S19L	THCA	1
Q68	S70I	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 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.

LBS	AAchange of nsSNV	Relative stability change
Q68	S70I	0.19370098
S19	S19L	-0.13138314

(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

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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.

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Phenotype information for RPRD1A

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0017661	Glomerulonephritis, IGA	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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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 status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RPRD1A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (PRO,SER,TYR,SER,PRO,THR,SER,PRO,SER,TYR,SER)	4jxt	A	S19 Q68

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Conservation information for LBS of RPRD1A

Multiple alignments for Q96P16 in multiple species

LBS	AA sequence	# species	Species
D65	LYLANDVIQNS	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
D65	LYVANDVSQNA	1	Caenorhabditis elegans
I110	GRVLSIWEERS	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
I110	GKLINVWKDRQ	1	Caenorhabditis elegans
N18	LSELSNSQQSV	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
N18	LTNLSNHPSSI	1	Caenorhabditis elegans
N64	FLYLANDVIQN	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
N64	LLYVANDVSQN	1	Caenorhabditis elegans
Q20	ELSNSQQSVQT	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Q20	NLSNHPSSIQT	1	Caenorhabditis elegans
Q68	ANDVIQNSKRK	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Q68	ANDVSQNARKT	1	Caenorhabditis elegans
R106	KKHLGRVLSIW	3	Homo sapiens, Bos taurus, Mus musculus
R106	EHAIGKLINVW	1	Caenorhabditis elegans
R106	KKHPGRVLSIW	1	Gallus gallus
R114	SIWEERSVYEN	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
R114	NVWKDRQIFTP	1	Caenorhabditis elegans
S19	SELSNSQQSVQ	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
S19	TNLSNHPSSIQ	1	Caenorhabditis elegans
V23	NSQQSVQTLSL	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
V23	NHPSSIQTTSA	1	Caenorhabditis elegans
Y61	L-TFLYLANDV	4	Homo sapiens, Gallus gallus, Bos taurus, Mus musculus
Y61	IVNLLYVANDV	1	Caenorhabditis elegans