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 SNX17
Gene summary
Basic gene Info.Gene symbolSNX17
Gene namesorting nexin 17
Synonyms-
CytomapUCSC genome browser: 2p23-p22
Type of geneprotein-coding
RefGenesNM_001267059.1,
NM_001267060.1,NM_001267061.1,NM_014748.3,NR_049782.1,
NR_049783.1,NR_049784.1,NR_049785.1,NR_049786.1,
NR_049787.1,NR_049788.1,
Descriptionsorting nexin-17
Modification date20141207
dbXrefs MIM : 605963
HGNC : HGNC
Ensembl : ENSG00000115234
HPRD : 05812
Vega : OTTHUMG00000097781
ProteinUniProt: Q15036
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SNX17
BioGPS: 9784
PathwayNCI Pathway Interaction Database: SNX17
KEGG: SNX17
REACTOME: SNX17
Pathway Commons: SNX17
ContextiHOP: SNX17
ligand binding site mutation search in PubMed: SNX17
UCL Cancer Institute: SNX17
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


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Ligand binding site mutations for SNX17
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
L346R345HBRCA1
L353Y352NBRCA1
Q377Q377EKIRC1
Q377C375YSTAD1
T316T316ASTAD1
K63L64PUCEC1
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 SNX17
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
L353Y352N-1.2528293
K63L64P-1.0798889
T316T316A-0.94949933
Q377C375Y-0.91596132
L346R345H-0.66826417
Q377Q377E-0.34456823
(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 SNX17 from PDB

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Differential gene expression and gene-gene network for SNX17
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 SNX17 and the right PPI network was created from samples without mutations in the LBS of SNX17. 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 SNX17
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 SNX17
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 SNX17 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SO4SULFATE3luiBK63
IIIPeptide ligand (THR,CYS,ILE,TYR,ASN,PRO,LEU,PHE,GLY,SER)4tknAT316
IIIPeptide ligand (GLY,THR,TYR,GLY,VAL,PHE,THR,ASN,ALA,ALA,TYR,ASP,PRO,THR,PRO)4gxbAT316 L346 L353
IIIPeptide ligand (THR,CYS,ILE,TYR,ASN,PRO,LEU,PHE,GLY)4tknBT316 L353 Q377
IIIPeptide ligand (THR,CYS,ILE,TYR,ASN,PRO,LEU,PHE,GLY)4tknCT316 L353 Q377


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Conservation information for LBS of SNX17
Multiple alignments for Q15036 in multiple species
LBSAA sequence# speciesSpecies
C320VTRMRCWRVTS5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
I370TSPQAIMMSIC4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
I370TSQQAIMMSIC1Danio rerio
K63AFPPKKLFSLT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K63AFPPKKIFTLT1Danio rerio
L346RGEVRLELAFE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
L346KCDVKLELAFE1Danio rerio
L353LAFEYLMSKDR5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
L383SMVDELMVKKS5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
M318FRVTRMRCWRV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
M318FKVTRMRCWRV1Danio rerio
M384MVDELMVKKSG5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
Q377MSICLQSMVDE5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
Q74PAEVEQRREQL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q74PAEVDQRREQL1Danio rerio
Q78EQRREQLEKYM4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q78DQRREQLEKYM1Danio rerio
R317SFRVTRMRCWR4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R317SFKVTRMRCWR1Danio rerio
R319RVTRMRCWRVT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R319KVTRMRCWRVT1Danio rerio
R322RMRCWRVTSS-4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R322RMRCWRVTSSQ1Danio rerio
S325CWRVTSS-VPL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S325CWRVTSSQVPV1Danio rerio
T316GSFRVTRMRCW4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T316GSFKVTRMRCW1Danio rerio
V315EGSFRVTRMRC4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V315EGSFKVTRMRC1Danio rerio
V323MRCWRVTSS-V4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V323MRCWRVTSSQV1Danio rerio
V380CLQSMVDELMV5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
W321TRMRCWRVTSS5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
W361KDRLQWVTITS5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus


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