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 PRMT5
Gene summary
Basic gene Info.Gene symbolPRMT5
Gene nameprotein arginine methyltransferase 5
SynonymsHRMT1L5|IBP72|JBP1|SKB1|SKB1Hs
CytomapUCSC genome browser: 14q11.2
Type of geneprotein-coding
RefGenesNM_001039619.2,
NM_001282953.1,NM_001282954.1,NM_001282955.1,NM_001282956.1,
NM_006109.4,
Description72 kDa ICln-binding proteinHMT1 hnRNP methyltransferase-like 5SKB1 homologhistone-arginine N-methyltransferase PRMT5jak-binding protein 1protein arginine N-methyltransferase 5shk1 kinase-binding protein 1 homolog
Modification date20141222
dbXrefs MIM : 604045
HGNC : HGNC
Ensembl : ENSG00000100462
HPRD : 04955
Vega : OTTHUMG00000028709
ProteinUniProt: O14744
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRMT5
BioGPS: 10419
PathwayNCI Pathway Interaction Database: PRMT5
KEGG: PRMT5
REACTOME: PRMT5
Pathway Commons: PRMT5
ContextiHOP: PRMT5
ligand binding site mutation search in PubMed: PRMT5
UCL Cancer Institute: PRMT5
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0035246peptidyl-arginine N-methylation15369763


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Ligand binding site mutations for PRMT5

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K333I332MBLCA1
Y334Q336RCOAD1
P311P311QLUAD1
Y334Q336EOV1
A366A366TUCEC1
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 PRMT5
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
K333I332M-1.3846526
P311P311Q-0.88699834
Y334Q336R-0.53554069
A366A366T-0.48825821
Y334Q336E-0.48347917
(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 PRMT5 from PDB

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Differential gene expression and gene-gene network for PRMT5
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 PRMT5 and the right PPI network was created from samples without mutations in the LBS of PRMT5. 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 PRMT5
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for PRMT5
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 PRMT5 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
3XVN-[(2S)-3-(3,4-DIHYDROISOQUINOLIN-2(1H)-YL)-2- HYDROXYPROPYL]-6-(OXETAN-3-YLAMINO)PYRIMIDINE-4- CARBOXAMIDE4x60AK333
3XVN-[(2S)-3-(3,4-DIHYDROISOQUINOLIN-2(1H)-YL)-2- HYDROXYPROPYL]-6-(OXETAN-3-YLAMINO)PYRIMIDINE-4- CARBOXAMIDE4x61AK333
3XVN-[(2S)-3-(3,4-DIHYDROISOQUINOLIN-2(1H)-YL)-2- HYDROXYPROPYL]-6-(OXETAN-3-YLAMINO)PYRIMIDINE-4- CARBOXAMIDE4x63AK333
0XU(2S,5S,6E)-2,5-DIAMINO-6-[(3S,4R,5R)-5-(6-AMINO-9H- PURIN-9-YL)-3,4-DIHYDROXYDIHYDROFURAN-2(3H)- YLIDENE]HEXANOIC ACID4gqbAK333 Y334
SFGSINEFUNGIN4x60AK333 Y334
SAMS-ADENOSYL-L-METHIONINE4x61AK333 Y334 A366
SAHS-ADENOSYL-L-HOMOCYSTEINE4x63AK333 Y334 A366
IIIPeptide ligand (ACE,SER,GLY,ARG,GLY,LYS,GLY,GLY,LYS)4gqbAP311


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Conservation information for LBS of PRMT5
Multiple alignments for O14744 in multiple species
LBSAA sequence# speciesSpecies
A366LMVLGAGRGPL3Homo sapiens, Mus musculus, Bos taurus
A366LMVVGAGRGPL2Arabidopsis thaliana, Oryza sativa subsp. japonica
A366VMLLGGGRGPL1Drosophila melanogaster
C449ELSPECLDGAQ4Homo sapiens, Mus musculus, Arabidopsis thaliana, Oryza sativa subsp. japonica
C449ELSPECLDGAL1Drosophila melanogaster
C449ELSPESLDGAQ1Bos taurus
D419TVVSSDMREWV3Homo sapiens, Mus musculus, Bos taurus
D419HIFSKDMRDFS1Drosophila melanogaster
D419TIISCDMRFWN1Arabidopsis thaliana
D419TIISSDMRCWE1Oryza sativa subsp. japonica
E392KLYAVEKNPNA2Homo sapiens, Bos taurus
E392KVYAVEKNPNA2Arabidopsis thaliana, Oryza sativa subsp. japonica
E392RLYIIEKNPNA1Drosophila melanogaster
E392RLYAVEKNPNA1Mus musculus
E435DIIVSELLGSF3Homo sapiens, Mus musculus, Bos taurus
E435DILVSELLGSF2Arabidopsis thaliana, Oryza sativa subsp. japonica
E435DIMVSELLGSF1Drosophila melanogaster
E444SFGDNELSPEC3Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa subsp. japonica
E444SFADNELSPEC2Homo sapiens, Mus musculus
E444SFADNELSPES1Bos taurus
F300NAYELFAKGYE3Homo sapiens, Mus musculus, Bos taurus
F300NCDKHMLNSYE1Drosophila melanogaster
F300SEQERIELGYR1Arabidopsis thaliana
F300PEQERFEINYR1Oryza sativa subsp. japonica
F327QTYEVFEKDPI3Homo sapiens, Mus musculus, Bos taurus
F327YTYEVFETDPV1Drosophila melanogaster
F327QTYETFERDSV1Arabidopsis thaliana
F327QTYETFEKDTV1Oryza sativa subsp. japonica
F577HSPGMFSWFPI3Homo sapiens, Mus musculus, Bos taurus
F577ATPNMFSWFPI2Arabidopsis thaliana, Oryza sativa subsp. japonica
F577HTPGMFSWFPM1Drosophila melanogaster
F580GMFSWFPILFP2Homo sapiens, Bos taurus
F580NMFSWFPIFFP2Arabidopsis thaliana, Oryza sativa subsp. japonica
F580GMFSWFPMFFA1Drosophila melanogaster
F580GMFSWFPIFFP1Mus musculus
G365VLMVLGAGRGP3Homo sapiens, Mus musculus, Bos taurus
G365VLMVVGAGRGP2Arabidopsis thaliana, Oryza sativa subsp. japonica
G365VVMLLGGGRGP1Drosophila melanogaster
G367MVLGAGRGPLV3Homo sapiens, Mus musculus, Bos taurus
G367MVVGAGRGPLV2Arabidopsis thaliana, Oryza sativa subsp. japonica
G367MLLGGGRGPLA1Drosophila melanogaster
G438VSELLGSFADN3Homo sapiens, Mus musculus, Bos taurus
G438VSELLGSFGDN3Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa subsp. japonica
K333EKDPIKYSQYQ3Homo sapiens, Mus musculus, Bos taurus
K333ETDPVKYKLYQ1Drosophila melanogaster
K333ERDSVKYIQYQ1Arabidopsis thaliana
K333EKDTVKYTQYQ1Oryza sativa subsp. japonica
K393LYAVEKNPNAV3Homo sapiens, Mus musculus, Bos taurus
K393VYAVEKNPNAV2Arabidopsis thaliana, Oryza sativa subsp. japonica
K393LYIIEKNPNAI1Drosophila melanogaster
L308GYEDYLQSPLQ3Homo sapiens, Mus musculus, Bos taurus
L308SYENMLEIPLQ1Drosophila melanogaster
L308GYRDFLQAPLQ1Arabidopsis thaliana
L308NYRDFLQSPLQ1Oryza sativa subsp. japonica
L312YLQSPLQPLMD3Homo sapiens, Mus musculus, Bos taurus
L312MLEIPLQPLCD1Drosophila melanogaster
L312FLQAPLQPLMD1Arabidopsis thaliana
L312FLQSPLQPLMD1Oryza sativa subsp. japonica
L315SPLQPLMDNLE4Homo sapiens, Mus musculus, Bos taurus, Oryza sativa subsp. japonica
L315IPLQPLCDNLD1Drosophila melanogaster
L315APLQPLMDNLE1Arabidopsis thaliana
L319PLMDNLESQTY3Homo sapiens, Mus musculus, Bos taurus
L319PLMDNLEAQTY2Arabidopsis thaliana, Oryza sativa subsp. japonica
L319PLCDNLDTYTY1Drosophila melanogaster
L371AGRGPLVNASL3Homo sapiens, Mus musculus, Bos taurus
L371AGRGPLVRASL2Arabidopsis thaliana, Oryza sativa subsp. japonica
L371GGRGPLARAVF1Drosophila melanogaster
L436IIVSELLGSFA3Homo sapiens, Mus musculus, Bos taurus
L436ILVSELLGSFG2Arabidopsis thaliana, Oryza sativa subsp. japonica
L436IMVSELLGSFG1Drosophila melanogaster
L437IVSELLGSFAD3Homo sapiens, Mus musculus, Bos taurus
L437LVSELLGSFGD2Arabidopsis thaliana, Oryza sativa subsp. japonica
L437MVSELLGSFGD1Drosophila melanogaster
M420VVSSDMREWVA3Homo sapiens, Mus musculus, Bos taurus
M420IFSKDMRDFSP1Drosophila melanogaster
M420IISCDMRFWNA1Arabidopsis thaliana
M420IISSDMRCWEA1Oryza sativa subsp. japonica
P311DYLQSPLQPLM3Homo sapiens, Mus musculus, Bos taurus
P311NMLEIPLQPLC1Drosophila melanogaster
P311DFLQAPLQPLM1Arabidopsis thaliana
P311DFLQSPLQPLM1Oryza sativa subsp. japonica
P314QSPLQPLMDNL4Homo sapiens, Mus musculus, Bos taurus, Oryza sativa subsp. japonica
P314EIPLQPLCDNL1Drosophila melanogaster
P314QAPLQPLMDNL1Arabidopsis thaliana
P370GAGRGPLVNAS3Homo sapiens, Mus musculus, Bos taurus
P370GAGRGPLVRAS2Arabidopsis thaliana, Oryza sativa subsp. japonica
P370GGGRGPLARAV1Drosophila melanogaster
Q309YEDYLQSPLQP3Homo sapiens, Mus musculus, Bos taurus
Q309YENMLEIPLQP1Drosophila melanogaster
Q309YRDFLQAPLQP1Arabidopsis thaliana
Q309YRDFLQSPLQP1Oryza sativa subsp. japonica
R421VSSDMREWVAP3Homo sapiens, Mus musculus, Bos taurus
R421FSKDMRDFSPP1Drosophila melanogaster
R421ISCDMRFWNAP1Arabidopsis thaliana
R421ISSDMRCWEAP1Oryza sativa subsp. japonica
S310EDYLQSPLQPL3Homo sapiens, Mus musculus, Bos taurus
S310ENMLEIPLQPL1Drosophila melanogaster
S310RDFLQAPLQPL1Arabidopsis thaliana
S310RDFLQSPLQPL1Oryza sativa subsp. japonica
S418VTVVSSDMREW3Homo sapiens, Mus musculus, Bos taurus
S418VHIFSKDMRDF1Drosophila melanogaster
S418VTIISCDMRFW1Arabidopsis thaliana
S418VTIISSDMRCW1Oryza sativa subsp. japonica
S439SELLGSFADNE3Homo sapiens, Mus musculus, Bos taurus
S439SELLGSFGDNE3Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa subsp. japonica
S578SPGMFSWFPIL2Homo sapiens, Bos taurus
S578TPNMFSWFPIF2Arabidopsis thaliana, Oryza sativa subsp. japonica
S578TPGMFSWFPMF1Drosophila melanogaster
S578SPGMFSWFPIF1Mus musculus
V503FEMPYVVRLHN3Homo sapiens, Mus musculus, Bos taurus
V503FDYGYVSLLKN1Drosophila melanogaster
V503FETAYVVKLHS1Arabidopsis thaliana
V503FETAYVVKLHR1Oryza sativa subsp. japonica
W579PGMFSWFPILF2Homo sapiens, Bos taurus
W579PNMFSWFPIFF2Arabidopsis thaliana, Oryza sativa subsp. japonica
W579PGMFSWFPMFF1Drosophila melanogaster
W579PGMFSWFPIFF1Mus musculus
Y304LFAKGYEDYLQ3Homo sapiens, Mus musculus, Bos taurus
Y304HMLNSYENMLE1Drosophila melanogaster
Y304RIELGYRDFLQ1Arabidopsis thaliana
Y304RFEINYRDFLQ1Oryza sativa subsp. japonica
Y307KGYEDYLQSPL3Homo sapiens, Mus musculus, Bos taurus
Y307NSYENMLEIPL1Drosophila melanogaster
Y307LGYRDFLQAPL1Arabidopsis thaliana
Y307INYRDFLQSPL1Oryza sativa subsp. japonica
Y324LESQTYEVFEK3Homo sapiens, Mus musculus, Bos taurus
Y324LDTYTYEVFET1Drosophila melanogaster
Y324LEAQTYETFER1Arabidopsis thaliana
Y324LEAQTYETFEK1Oryza sativa subsp. japonica
Y334KDPIKYSQYQQ3Homo sapiens, Mus musculus, Bos taurus
Y334TDPVKYKLYQD1Drosophila melanogaster
Y334RDSVKYIQYQR1Arabidopsis thaliana
Y334KDTVKYTQYQR1Oryza sativa subsp. japonica


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