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 ATL1
Gene summary
Basic gene Info.Gene symbolATL1
Gene nameatlastin GTPase 1
SynonymsAD-FSP|FSP1|GBP3|HSN1D|SPG3|SPG3A|atlastin1
CytomapUCSC genome browser: 14q22.1
Type of geneprotein-coding
RefGenesNM_001127713.1,
NM_015915.4,NM_181598.3,
DescriptionGBP-3GTP-binding protein 3atlastin-1brain-specific GTP-binding proteinguanine nucleotide-binding protein 3guanylate-binding protein 3hGBP3spastic paraplegia 3 protein A
Modification date20141219
dbXrefs MIM : 606439
HGNC : HGNC
Ensembl : ENSG00000198513
HPRD : 05918
Vega : OTTHUMG00000140297
ProteinUniProt: Q8WXF7
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ATL1
BioGPS: 51062
PathwayNCI Pathway Interaction Database: ATL1
KEGG: ATL1
REACTOME: ATL1
Pathway Commons: ATL1
ContextiHOP: ATL1
ligand binding site mutation search in PubMed: ATL1
UCL Cancer Institute: ATL1
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:0006184GTP catabolic process14506257
GO:0007029endoplasmic reticulum organization19665976
GO:0051260protein homooligomerization14506257


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Ligand binding site mutations for ATL1
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
D146D146GCOAD1
G149G149RLUAD1
F293F293LOV1
D146M145ISKCM1
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 ATL1
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
F293F293L-1.1597337
D146M145I-1.1214966
D146D146G-0.90699657
G149G149R-0.7766481
(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 ATL1 from PDB

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Differential gene expression and gene-gene network for ATL1
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 ATL1 and the right PPI network was created from samples without mutations in the LBS of ATL1. 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 ATL1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C2931355Spastic paraplegia 3, autosomal dominant2Biomarker, GeneticVariation

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

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Pharmacological information for ATL1
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 ATL1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
MGMAGNESIUM(2+)3q5eAD146
MGMAGNESIUM(2+)3q5eGD146
MGMAGNESIUM(2+)3qofAD146
MGMAGNESIUM(2+)3qofBD146
MGMAGNESIUM(2+)3qofCD146
MGMAGNESIUM(2+)3qofDD146
MGMAGNESIUM(2+)4idpCD146
MGMAGNESIUM(2+)4idpDD146
MGMAGNESIUM(2+)4idqDD146
GDPGUANOSINE-5'-DIPHOSPHATE4idqBF293
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4idnAG149
ALFTETRAFLUOROALUMINATE(1-)4idoAG149
ALFTETRAFLUOROALUMINATE(1-)4idoBG149
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4idpAG149
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4idpDG149
ALFTETRAFLUOROALUMINATE(1-)4idqAG149
ALFTETRAFLUOROALUMINATE(1-)4idqBG149
ALFTETRAFLUOROALUMINATE(1-)4idqCG149
ALFTETRAFLUOROALUMINATE(1-)4idqDG149
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4idnBG149 F293
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4idpBG149 F293


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Conservation information for LBS of ATL1
Multiple alignments for Q8WXF7 in multiple species
LBSAA sequence# speciesSpecies
A277PGLKVATNPNF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D146AVLLMDTQGTF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D218IFLVRDWSFPY4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E117WRGGSERETTG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
E119GGSERETTGIQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F282ATNPNFDGKLK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F293EIDDEFIKNLK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F76SVAGAFRKGKS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F82RKGKSFLMDFM4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G114GFSWRGGSERE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G149LMDTQGTFDSQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G79GAFRKGKSFLM4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H271CFLLPHPGLKV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K78AGAFRKGKSFL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K80AFRKGKSFLMD4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N279LKVATNPNFDG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P272FLLPHPGLKVA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P280KVATNPNFDGK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q124ETTGIQIWSEI2Homo sapiens, Bos taurus
Q124ETTGIQIWSEV2Mus musculus, Rattus norvegicus
Q148LLMDTQGTFDS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R113TGFSWRGGSER4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R118RGGSERETTGI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R217LIFLVRDWSFP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R77VAGAFRKGKSF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S81FRKGKSFLMDF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
T120GSERETTGIQI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V276HPGLKVATNPN4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
W112LTGFSWRGGSE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus


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