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 RFC1
Gene summary
Basic gene Info.Gene symbolRFC1
Gene namereplication factor C (activator 1) 1, 145kDa
CytomapUCSC genome browser: 4p14-p13
Type of geneprotein-coding
DescriptionA1 140 kDa subunitDNA-binding protein PO-GAMHC binding factor, betaRF-C 140 kDa subunitactivator 1 140 kDa subunitactivator 1 large subunitactivator 1 subunit 1replication factor C 140 kDa subunitreplication factor C large subunitreplication fact
Modification date20141207
dbXrefs MIM : 102579
Ensembl : ENSG00000035928
HPRD : 00024
Vega : OTTHUMG00000099363
ProteinUniProt: P35251
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RFC1
BioGPS: 5981
PathwayNCI Pathway Interaction Database: RFC1
Pathway Commons: RFC1
ContextiHOP: RFC1
ligand binding site mutation search in PubMed: RFC1
UCL Cancer Institute: RFC1
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 RFC1
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 RFC1
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 RFC1 from PDB

Differential gene expression and gene-gene network for RFC1
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 RFC1 and the right PPI network was created from samples without mutations in the LBS of RFC1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for RFC1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0029463Osteosarcoma6Biomarker, GeneticVariation
umls:C0009375Colonic Neoplasms1Biomarker

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

Pharmacological information for RFC1
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 RFC1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids2k7fAK375 R383 R423
NUCNucleic Acids2k7fAV437 R452

Conservation information for LBS of RFC1
Multiple alignments for P35251 in multiple species
LBSAA sequence# speciesSpecies
D453LVMGRDSGQSK2Homo sapiens, Mus musculus
D453LVVGEEAGPKK1Drosophila melanogaster
D453VVLGDEAGPKK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D453ILLGENAGPRK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G416IFVITGVLESI1Homo sapiens
G416TFVVTGVLESM1Drosophila melanogaster
G416TFVITGVLESI1Mus musculus
G416TIVFTGVLPTL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G416SFVITGILETL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G439GGKVTGNVSKK2Homo sapiens, Mus musculus
G439GGKVMTVVGKK1Drosophila melanogaster
G439GARVTKSISSK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G439GGKVTGAPSVR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G455MGRDSGQSKSD2Homo sapiens, Mus musculus
G455VGEEAGPKKLA1Drosophila melanogaster
G455LGDEAGPKKLE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G455LGENAGPRKVE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I414GLIFVITGVLE1Homo sapiens
I414GLTFVVTGVLE1Drosophila melanogaster
I414GLTFVITGVLE1Mus musculus
I414GLTIVFTGVLP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I414GISFVITGILE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K375EDSEKKRTNYQ2Homo sapiens, Mus musculus
K375ERHERKRASAV1Drosophila melanogaster
K375NVHVKENAKFD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K375-----------1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K436ERYGGKVTGNV2Homo sapiens, Mus musculus
K436KEYGGKVMTVV1Drosophila melanogaster
K436KRYGARVTKSI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K436KQYGGKVTGAP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K458DSGQSKSDKAA2Homo sapiens, Mus musculus
K458EAGPKKLAVAE1Drosophila melanogaster
K458EAGPKKLEKIK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K458NAGPRKVETIK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L386AYRSYLNREGP2Homo sapiens, Mus musculus
L386LYQKYKNRSSC1Drosophila melanogaster
L386-FKSANSNADP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L386---FYERAATT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N440GKVTGNVSKKT2Homo sapiens, Mus musculus
N440GKVMTVVGKKL1Drosophila melanogaster
N440ARVTKSISSKT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N440GKVTGAPSVRT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q456GRDSGQSKSDK2Homo sapiens, Mus musculus
Q456GEEAGPKKLAV1Drosophila melanogaster
Q456GDEAGPKKLEK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q456GENAGPRKVET1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R383NYQAYRSYLNR2Homo sapiens, Mus musculus
R383SAVLYQKYKNR1Drosophila melanogaster
R383KFD-FKSANSN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R383------FYERA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R388RSYLNREGPKA2Homo sapiens, Mus musculus
R388QKYKNRSSCLN1Drosophila melanogaster
R388KSANSNADPDE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R388-FYERAATTQT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R423LESIERDEAKS2Homo sapiens, Mus musculus
R423LESMEREEAES1Drosophila melanogaster
R423LPTLERGASEA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R423LETLTRQEATD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R452YLVMGRDSGQS2Homo sapiens, Mus musculus
R452YLVVGEEAGPK1Drosophila melanogaster
R452VVVLGDEAGPK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R452FILLGENAGPR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S454VMGRDSGQSKS2Homo sapiens, Mus musculus
S454VVGEEAGPKKL1Drosophila melanogaster
S454VLGDEAGPKKL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S454LLGENAGPRKV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S457RDSGQSKSDKA2Homo sapiens, Mus musculus
S457EEAGPKKLAVA1Drosophila melanogaster
S457DEAGPKKLEKI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S457ENAGPRKVETI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T415LIFVITGVLES1Homo sapiens
T415LTFVVTGVLES1Drosophila melanogaster
T415LTFVITGVLES1Mus musculus
T415LTIVFTGVLPT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T415ISFVITGILET1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T438YGGKVTGNVSK2Homo sapiens, Mus musculus
T438YGGKVMTVVGK1Drosophila melanogaster
T438YGARVTKSISS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T438YGGKVTGAPSV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V437RYGGKVTGNVS2Homo sapiens, Mus musculus
V437EYGGKVMTVVG1Drosophila melanogaster
V437RYGARVTKSIS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V437QYGGKVTGAPS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y379KKRTNYQAYRS2Homo sapiens, Mus musculus
Y379RKRASAVLYQK1Drosophila melanogaster
Y379KENAKFD-FKS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y379----------F1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y385QAYRSYLNREG2Homo sapiens, Mus musculus
Y385VLYQKYKNRSS1Drosophila melanogaster
Y385D-FKSANSNAD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y385----FYERAAT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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