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 PRMT3
Gene summary
Basic gene Info.Gene symbolPRMT3
Gene nameprotein arginine methyltransferase 3
CytomapUCSC genome browser: 11p15.1
Type of geneprotein-coding
DescriptionHMT1 hnRNP methyltransferase-like 3heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 3protein arginine N-methyltransferase 3
Modification date20141207
dbXrefs MIM : 603190
Ensembl : ENSG00000185238
HPRD : 11934
Vega : OTTHUMG00000166022
ProteinUniProt: O60678
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRMT3
BioGPS: 10196
PathwayNCI Pathway Interaction Database: PRMT3
Pathway Commons: PRMT3
ContextiHOP: PRMT3
ligand binding site mutation search in PubMed: PRMT3
UCL Cancer Institute: PRMT3
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0031397negative regulation of protein ubiquitination18573314

Ligand binding site mutations for PRMT3

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 PRMT3
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 PRMT3 from PDB
PDB IDPDB titlePDB structure
2FYTHuman HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae) protein

Differential gene expression and gene-gene network for PRMT3
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 PRMT3 and the right PPI network was created from samples without mutations in the LBS of PRMT3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PRMT3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for PRMT3
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
ExperimentalDB01752S-Adenosyl-L-HomocysteineSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PRMT3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PRMT3
Multiple alignments for O60678 in multiple species
LBSAA sequence# speciesSpecies
A450TAMCTAVAGYF2Mus musculus, Rattus norvegicus
A450TSMCTAIAGYF1Homo sapiens
A450EGPLCAFTLWF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C264VLDVGCGTGIL4Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Mus musculus, Rattus norvegicus
D285KVIAVDQSEIL2Mus musculus, Rattus norvegicus
D285KVLGVDQSEIL1Homo sapiens
D285KVYAVDNSDII1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D372LVAVSDVSKHA2Mus musculus, Rattus norvegicus
D372LVAVSDVNKHA1Homo sapiens
D372LTATTNTELLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E314IKGKIEEVSLP2Mus musculus, Rattus norvegicus
E314IKGKIEEVHLP1Homo sapiens
E314IRGKIEDISLP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E329DVIISEWMGYF3Homo sapiens, Mus musculus, Rattus norvegicus
E329DIIISEWMGYA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E405PEAVVEVVDHK2Mus musculus, Rattus norvegicus
E405PEAVVEVLDPK1Homo sapiens
E405KGVSVQVVPQT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G263VVLDVGCGTGI3Homo sapiens, Mus musculus, Rattus norvegicus
G263TVLDVGCGTGI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G265LDVGCGTGILS4Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Mus musculus, Rattus norvegicus
G311IVLIKGKIEEV2Mus musculus, Rattus norvegicus
G311ITLIKGKIEEV1Homo sapiens
G311ITFIRGKIEDI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H230GHYGIHEEMLK3Homo sapiens, Mus musculus, Rattus norvegicus
H230AGNDIHFLMLN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H376SDVSKHADRIA2Mus musculus, Rattus norvegicus
H376SDVNKHADRIA1Homo sapiens
H376TNTELLEEPID1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I268GCGTGILSMFA3Homo sapiens, Mus musculus, Rattus norvegicus
I268GCGTGILSMFC1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I313LIKGKIEEVSL2Mus musculus, Rattus norvegicus
I313LIKGKIEEVHL1Homo sapiens
I313FIRGKIEDISL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K312VLIKGKIEEVS2Mus musculus, Rattus norvegicus
K312TLIKGKIEEVH1Homo sapiens
K312TFIRGKIEDIS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K375VSDVSKHADRI2Mus musculus, Rattus norvegicus
K375VSDVNKHADRI1Homo sapiens
K375TTNTELLEEPI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L269CGTGILSMFAA3Homo sapiens, Mus musculus, Rattus norvegicus
L269CGTGILSMFCA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L407AVVEVVDHKTL2Mus musculus, Rattus norvegicus
L407AVVEVLDPKTL1Homo sapiens
L407VSVQVVPQTYV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L486KQTVFLL-EKP2Homo sapiens, Mus musculus
L486KQCVLLLRNRP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L486KQTIFLL-EKP1Rattus norvegicus
M233GIHEEMLKDKV2Mus musculus, Rattus norvegicus
M233GIHEEMLKDKI1Homo sapiens
M233DIHFLMLNDSV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M340LLFESMLDSVL3Homo sapiens, Mus musculus, Rattus norvegicus
M340LTFESMIDSVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q286VIAVDQSEILY2Mus musculus, Rattus norvegicus
Q286VLGVDQSEILY1Homo sapiens
Q286VYAVDNSDIIQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R239LKDKVRTESYR2Mus musculus, Rattus norvegicus
R239LKDKIRTESYR1Homo sapiens
R239LNDSVRTEGYR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R379SKHADRIAFWD2Mus musculus, Rattus norvegicus
R379NKHADRIAFWD1Homo sapiens
R379ELLEEPIDFWS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S287IAVDQSEILYQ2Mus musculus, Rattus norvegicus
S287LGVDQSEILYQ1Homo sapiens
S287YAVDNSDIIQM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S343ESMLDSVLYAK3Homo sapiens, Mus musculus, Rattus norvegicus
S343ESMIDSVLVAR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T449KTAMCTAVAGY2Mus musculus, Rattus norvegicus
T449RTSMCTAIAGY1Homo sapiens
T449NEGPLCAFTLW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V370ISLVAVSDVSK2Mus musculus, Rattus norvegicus
V370ISLVAVSDVNK1Homo sapiens
V370LVLTATTNTEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V403VIPEAVVEVVD2Mus musculus, Rattus norvegicus
V403VIPEAVVEVLD1Homo sapiens
V403SYKGVSVQVVP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y224VYFSSYGHYGI3Homo sapiens, Mus musculus, Rattus norvegicus
Y224YYFESYAGNDI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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