mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

Download

 Statistics

Help

About Us
Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SNRPD2
Gene summary
Basic gene Info.Gene symbolSNRPD2
Gene namesmall nuclear ribonucleoprotein D2 polypeptide 16.5kDa
SynonymsSMD2|SNRPD1|Sm-D2
CytomapUCSC genome browser: 19q13.2
Type of geneprotein-coding
RefGenesNM_004597.5,
NM_177542.2,
Descriptionsmall nuclear ribonucleoprotein Sm D2snRNP core protein D2
Modification date20141207
dbXrefs MIM : 601061
HGNC : HGNC
Ensembl : ENSG00000125743
HPRD : 03038
Vega : OTTHUMG00000182130
ProteinUniProt: P62316
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNRPD2
BioGPS: 6633
PathwayNCI Pathway Interaction Database: SNRPD2
KEGG: SNRPD2
REACTOME: SNRPD2
Pathway Commons: SNRPD2
ContextiHOP: SNRPD2
ligand binding site mutation search in PubMed: SNRPD2
UCL Cancer Institute: SNRPD2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000387spliceosomal snRNP assembly18984161


Top
Ligand binding site mutations for SNRPD2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K79K79NHNSC1
E15E14AHNSC1
I107V106FLUSC1
K82G81DSTAD1
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.


Top
Protein structure related information for SNRPD2
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
I107V106F-1.1545847
K79K79N-0.81598262
K82G81D-0.80012652
E15E14A-0.047465122
(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 SNRPD2 from PDB

Top
Differential gene expression and gene-gene network for SNRPD2
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 SNRPD2 and the right PPI network was created from samples without mutations in the LBS of SNRPD2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Top

Top
Phenotype information for SNRPD2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Top
Pharmacological information for SNRPD2
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 SNRPD2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids4pjoDE15
NUCNucleic Acids4pjoRE15
NUCNucleic Acids4pjorE15


Top
Conservation information for LBS of SNRPD2
Multiple alignments for P62316 in multiple species
LBSAA sequence# speciesSpecies
D104MFLRGDSVIVV3Homo sapiens, Bos taurus, Mus musculus
D104MFLRGDSVILV2Caenorhabditis elegans, Drosophila melanogaster
D104LFLRGDSVIVV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D104MFLRGDGVVLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E10NKPKSEMTPEE3Homo sapiens, Bos taurus, Mus musculus
E10DRPKHELSRAE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E10DKPRSELSEIE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E10AKPRSEMTAEE1Caenorhabditis elegans
E10VKPKSELTPEE1Drosophila melanogaster
E15EMTPEELQKRE3Homo sapiens, Bos taurus, Mus musculus
E15ELSRAELEELE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E15ELSEIELARLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E15EMTAEELAAKE1Caenorhabditis elegans
E15ELTPEELARQE1Drosophila melanogaster
F24REEEEFNTGPL3Homo sapiens, Bos taurus, Mus musculus
F24LEEFEFKHGPM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F24LEEYEFSAGPL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F24KEDEEFNVGPL1Caenorhabditis elegans
F24QEEEEFNTGPL1Drosophila melanogaster
G103KMFLRGDSVIV3Homo sapiens, Bos taurus, Mus musculus
G103KMFLRGDSVIL2Caenorhabditis elegans, Drosophila melanogaster
G103KLFLRGDSVIV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G103KMFLRGDGVVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H62KAFDRHCNMVL6Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
H62KAFDRHSNMVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I107RGDSVIVVLRN3Homo sapiens, Bos taurus, Mus musculus
I107RGDSVIVVLKT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I107RGDGVVLVVRI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I107RGDSVILVVKN1Caenorhabditis elegans
I107RGDSVILVLRN1Drosophila melanogaster
K50NCRNNKKLLGR5Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
K50SLRNNHKIIAR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K50NCRNNKKLLAR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K79WTEVPKSGKGK3Homo sapiens, Bos taurus, Mus musculus
K79WTE-------K1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K79WTEKKRTASGK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K79WTEVPKTGKGK1Caenorhabditis elegans
K79WTELPRTGKGK1Drosophila melanogaster
K82VPKSGKGKKKS3Homo sapiens, Bos taurus, Mus musculus
K82-------KKGK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K82KKRTASGKKG-1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K82VPKTGKGKKKA1Caenorhabditis elegans
K82LPRTGKGKKKV1Drosophila melanogaster
N25EEEEFNTGPLS4Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster
N25EEFEFKHGPMS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N25EEYEFSAGPLS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N25EDEEFNVGPLS1Caenorhabditis elegans
N48LINCRNNKKLL6Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
N48IISLRNNHKII1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N49INCRNNKKLLG5Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
N49ISLRNNHKIIA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N49INCRNNKKLLA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N64FDRHCNMVLEN6Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
N64FDRHSNMVLEN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P28EFNTGPLSVLT4Homo sapiens, Bos taurus, Mus musculus, Drosophila melanogaster
P28EFKHGPMSLIN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P28EFSAGPLSVLQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P28EFNVGPLSILT1Caenorhabditis elegans
Q17TPEELQKREEE3Homo sapiens, Bos taurus, Mus musculus
Q17SRAELEELEEF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q17SEIELARLEEY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q17TAEELAAKEDE1Caenorhabditis elegans
Q17TPEELARQEEE1Drosophila melanogaster
R102SKMFLRGDSVI5Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
R102SKLFLRGDSVI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R102SKMFLRGDGVV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R47VLINCRNNKKL6Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
R47VIISLRNNHKI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R61VKAFDRHCNMV6Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Caenorhabditis elegans, Bos taurus, Mus musculus, Drosophila melanogaster
R61VKAFDRHSNMV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)


Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas