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mutLBSgeneDB |
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| Gene summary for ATRX |
 Gene summary |
| Basic gene Info. | Gene symbol | ATRX |
| Gene name | alpha thalassemia/mental retardation syndrome X-linked | |
| Synonyms | ATR2|JMS|MRXHF1|RAD54|RAD54L|SFM1|SHS|XH2|XNP|ZNF-HX | |
| Cytomap | UCSC genome browser: Xq21.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000489.4, NM_138270.3,NM_138271.1, | |
| Description | ATP-dependent helicase ATRXDNA dependent ATPase and helicaseX-linked helicase IIX-linked nuclear proteinZinc finger helicasealpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)helicase 2, X-linkedtranscriptional reg | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 300032 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000085224 | ||
| HPRD : 02069 | ||
| Vega : OTTHUMG00000022686 | ||
| Protein | UniProt: P46100 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_ATRX | |
| BioGPS: 546 | ||
| Pathway | NCI Pathway Interaction Database: ATRX | |
| KEGG: ATRX | ||
| REACTOME: ATRX | ||
| Pathway Commons: ATRX | ||
| Context | iHOP: ATRX | |
| ligand binding site mutation search in PubMed: ATRX | ||
| UCL Cancer Institute: ATRX | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0006200 | ATP catabolic process | 12953102 | GO:0006334 | nucleosome assembly | 20651253 | GO:0006338 | chromatin remodeling | 20651253 |
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| Ligand binding site mutations for ATRX |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Q219 | C220W | PRAD | 1 | N261,E259 | N260H | STAD | 1 |
| 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 ATRX |
| 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 |
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| 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. |
| LBS | AAchange of nsSNV | Relative stability change | E259 | N260H | -1.3618585 | N261 | N260H | -1.3618585 | Q219 | C220W | -0.55253945 |
| (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 ATRX from PDB |
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| Differential gene expression and gene-gene network for ATRX |
| 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) |
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| Phenotype information for ATRX |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1845055 | ATR-X syndrome | 33 | Biomarker, GeneticVariation |
| umls:C1136249 | Mental Retardation, X-Linked | 12 | Biomarker |
| umls:C0017638 | Glioma | 10 | Biomarker |
| umls:C0026986 | Myelodysplastic Syndromes | 9 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0206754 | Neuroendocrine Tumors | 3 | Biomarker |
| umls:C0027819 | Neuroblastoma | 3 | Biomarker |
| umls:C0585216 | Alpha-Thalassemia Myelodysplasia Syndrome | 1 | Biomarker, GeneticVariation |
| umls:C0010417 | Cryptorchidism | 1 | Biomarker |
| umls:C0010606 | Carcinoma, Adenoid Cystic | 1 | Biomarker |
| umls:C0376634 | Craniofacial Abnormalities | 1 | Biomarker |
| umls:C0018273 | Growth Disorders | 1 | Biomarker |
| umls:C0030297 | Pancreatic Neoplasms | 1 | Biomarker |
| umls:C0030846 | Penile Diseases | 1 | Biomarker |
| umls:C0039978 | Thoracic Diseases | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for ATRX |
| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of ATRX go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA) | 3qlc | B | E259 | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER,THR,GLY,GLY,LYS,ALA) | 2lbm | A | Q219 | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER) | 3ql9 | A | Q219 | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER) | 3qla | A | Q219 | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER) | 3qla | D | Q219 E259 N261 |
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| Conservation information for LBS of ATRX |
| Multiple alignments for P46100 in multiple species |
| LBS | AA sequence | # species | Species | A224 | QCRWCAEGGNL | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C171 | HGIVSCTACGQ | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C174 | VSCTACGQQVN | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C197 | LQVLICKNCFK | 2 | Homo sapiens, Pan troglodytes | C197 | LKVLICKNCFK | 1 | Mus musculus | C200 | LICKNCFKYYM | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C231 | GGNLICCDFCH | 3 | Homo sapiens, Mus musculus, Pan troglodytes | C232 | GNLICCDFCHN | 3 | Homo sapiens, Mus musculus, Pan troglodytes | D207 | KYYMSDDISRD | 3 | Homo sapiens, Mus musculus, Pan troglodytes | D208 | YYMSDDISRDS | 3 | Homo sapiens, Mus musculus, Pan troglodytes | D212 | DDISRDSDGMD | 3 | Homo sapiens, Mus musculus, Pan troglodytes | D217 | DSDGMDEQCRW | 3 | Homo sapiens, Mus musculus, Pan troglodytes | D233 | NLICCDFCHNA | 3 | Homo sapiens, Mus musculus, Pan troglodytes | E218 | SDGMDEQCRWC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | E225 | CRWCAEGGNLI | 3 | Homo sapiens, Mus musculus, Pan troglodytes | E259 | STIMDENNQWY | 3 | Homo sapiens, Mus musculus, Pan troglodytes | G226 | RWCAEGGNLIC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | G227 | WCAEGGNLICC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | I209 | YMSDDISRDSD | 3 | Homo sapiens, Mus musculus, Pan troglodytes | I230 | EGGNLICCDFC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | I256 | KELSTIMDENN | 3 | Homo sapiens, Mus musculus, Pan troglodytes | L229 | AEGGNLICCDF | 3 | Homo sapiens, Mus musculus, Pan troglodytes | M216 | RDSDGMDEQCR | 3 | Homo sapiens, Mus musculus, Pan troglodytes | M257 | ELSTIMDENNQ | 3 | Homo sapiens, Mus musculus, Pan troglodytes | N228 | CAEGGNLICCD | 3 | Homo sapiens, Mus musculus, Pan troglodytes | N261 | IMDENNQWYCY | 3 | Homo sapiens, Mus musculus, Pan troglodytes | Q219 | DGMDEQCRWCA | 3 | Homo sapiens, Mus musculus, Pan troglodytes | S206 | FKYYMSDDISR | 3 | Homo sapiens, Mus musculus, Pan troglodytes | W263 | DENNQWYCYIC | 3 | Homo sapiens, Mus musculus, Pan troglodytes | Y203 | KNCFKYYMSDD | 3 | Homo sapiens, Mus musculus, Pan troglodytes | Y204 | NCFKYYMSDDI | 3 | Homo sapiens, Mus musculus, Pan troglodytes |
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