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 SYN3
Gene summary
Basic gene Info.Gene symbolSYN3
Gene namesynapsin III
CytomapUCSC genome browser: 22q12.3
Type of geneprotein-coding
DescriptioncN28H9.2 (synapsin III)synapsin-3
Modification date20141207
dbXrefs MIM : 602705
Ensembl : ENSG00000185666
HPRD : 04083
Vega : OTTHUMG00000031004
ProteinUniProt: O14994
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SYN3
BioGPS: 8224
PathwayNCI Pathway Interaction Database: SYN3
Pathway Commons: SYN3
ContextiHOP: SYN3
ligand binding site mutation search in PubMed: SYN3
UCL Cancer Institute: SYN3
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 SYN3
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 SYN3
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 SYN3 from PDB

Differential gene expression and gene-gene network for SYN3
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 SYN3 and the right PPI network was created from samples without mutations in the LBS of SYN3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for SYN3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for SYN3
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 SYN3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ANPAMP-PNP2p0aAE284 W314 N317 E365
ANPAMP-PNP2p0aBE284 W314 N317 E365

Conservation information for LBS of SYN3
Multiple alignments for O14994 in multiple species
LBSAA sequence# speciesSpecies
A252IKLGHAHAGMG2Mus musculus, Rattus norvegicus
A252VKLGHAHAGMG1Homo sapiens
A254LGHAHAGMGKI3Homo sapiens, Mus musculus, Rattus norvegicus
A285YATTEAFIDSK3Homo sapiens, Mus musculus, Rattus norvegicus
A316SGNWKANTGSA3Homo sapiens, Mus musculus, Rattus norvegicus
D292IDSKYDIRIQK3Homo sapiens, Mus musculus, Rattus norvegicus
E284TYATTEAFIDS3Homo sapiens, Mus musculus, Rattus norvegicus
E365RDYIIEVMDSS3Homo sapiens, Mus musculus, Rattus norvegicus
G255GHAHAGMGKIK3Homo sapiens, Mus musculus, Rattus norvegicus
H253KLGHAHAGMGK3Homo sapiens, Mus musculus, Rattus norvegicus
I287TTEAFIDSKYD3Homo sapiens, Mus musculus, Rattus norvegicus
I364GRDYIIEVMDS3Homo sapiens, Mus musculus, Rattus norvegicus
K204YNFCSKPWVFS3Homo sapiens, Mus musculus, Rattus norvegicus
K248FPVVIKLGHAH2Mus musculus, Rattus norvegicus
K248FPVVVKLGHAH1Homo sapiens
K258HAGMGKIKVEN3Homo sapiens, Mus musculus, Rattus norvegicus
K315ISGNWKANTGS3Homo sapiens, Mus musculus, Rattus norvegicus
K352DICAVKAVHSK3Homo sapiens, Mus musculus, Rattus norvegicus
N317GNWKANTGSAM3Homo sapiens, Mus musculus, Rattus norvegicus
V246PNFPVVIKLGH2Mus musculus, Rattus norvegicus
V246PHFPVVVKLGH1Homo sapiens
W314SISGNWKANTG3Homo sapiens, Mus musculus, Rattus norvegicus

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