mutLBSgeneDB |
Gene summary for LMO2 |
Gene summary |
Basic gene Info. | Gene symbol | LMO2 |
Gene name | LIM domain only 2 (rhombotin-like 1) | |
Synonyms | RBTN2|RBTNL1|RHOM2|TTG2 | |
Cytomap | UCSC genome browser: 11p13 | |
Type of gene | protein-coding | |
RefGenes | NM_001142315.1, NM_001142316.1,NM_005574.3, | |
Description | LIM domain only protein 2LMO-2T-cell translocation gene 2T-cell translocation protein 2cysteine-rich protein TTG-2rhombotin 2rhombotin-2rhombotin-like 1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 180385 | |
HGNC : HGNC | ||
Ensembl : ENSG00000135363 | ||
HPRD : 01586 | ||
Vega : OTTHUMG00000157176 | ||
Protein | UniProt: P25791 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LMO2 | |
BioGPS: 4005 | ||
Pathway | NCI Pathway Interaction Database: LMO2 | |
KEGG: LMO2 | ||
REACTOME: LMO2 | ||
Pathway Commons: LMO2 | ||
Context | iHOP: LMO2 | |
ligand binding site mutation search in PubMed: LMO2 | ||
UCL Cancer Institute: LMO2 | ||
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:0042789 | mRNA transcription from RNA polymerase II promoter | 16314316 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 16314316 | GO:0097067 | cellular response to thyroid hormone stimulus | 19375645 |
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Ligand binding site mutations for LMO2 |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | R81 | R81W | BRCA | 1 | E145 | E145K | COAD | 1 | C125 | Q126E | LUAD | 1 | R40 | R40S | LUAD | 1 | G132 | G132A | LUAD | 1 | R69 | R69L | LUSC | 1 | D147 | D147N | SKCM | 1 | R102 | R102C | SKCM | 1 | C125 | A124V | SKCM | 1 | E145 | E145K | SKCM | 1 | R102 | R102H | STAD | 1 | C130 | C130R | STAD | 1 | R81 | R81L | STAD | 1 | E105 | E105D | UCEC | 1 | I101 | I101M | UCEC | 1 | C33 | Q35H | UCEC | 1 | G132 | G132C | UCEC | 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 LMO2 |
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. |
LBS | AAchange of nsSNV | Relative stability change | C130 | C130R | -1.2825234 | R40 | R40S | -1.1377328 | R102 | R102H | -1.0546466 | R81 | R81W | -0.92136437 | I101 | I101M | -0.87440781 | R102 | R102C | -0.79622962 | E105 | E105D | -0.73240148 | E145 | E145K | -0.66684043 | R81 | R81L | -0.6480299 | D147 | D147N | -0.6444738 | C33 | Q35H | -0.61341812 | C125 | A124V | -0.54450124 | G132 | G132A | -0.4997136 | G132 | G132C | -0.26120474 | C125 | Q126E | -0.076074925 | R69 | R69L | -0.009839719 |
(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 LMO2 from PDB |
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Differential gene expression and gene-gene network for LMO2 |
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 LMO2 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C1961099 | Precursor T-Cell Lymphoblastic Leukemia-Lymphoma | 22 | Biomarker, GeneticVariation |
umls:C0023492 | Leukemia, T-Cell | 9 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for LMO2 |
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 status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of LMO2 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2xjy | A | C125 D147 | ZN | ZINC(2+) | 2ypa | C | C125 D147 | ZN | ZINC(2+) | 4kfz | A | C125 D147 | ZN | ZINC(2+) | 4kfz | B | C125 D147 | ZN | ZINC(2+) | 2xjy | A | C33 | ZN | ZINC(2+) | 2ypa | C | C33 | ZN | ZINC(2+) | 4kfz | A | C33 | ZN | ZINC(2+) | 4kfz | B | C33 | III | Peptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU,GLU,ASN,THR) | 2xjz | A | R102 | III | Peptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG) | 2xjz | C | R102 | III | Peptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU,GLU,ASN,THR) | 2xjz | D | R102 | III | Peptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU) | 2xjz | E | R102 |
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Conservation information for LBS of LMO2 |
Multiple alignments for P25791 in multiple species |
LBS | AA sequence | # species | Species | A103 | DKRIRAYEMTM | 1 | Homo sapiens | A103 | EKRIRAFEMTM | 1 | Danio rerio | A103 | DKRIRAFEMTM | 1 | Xenopus tropicalis | C122 | LECFKCAACQK | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C125 | FKCAACQKHFC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C130 | CQKHFCVGDRY | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C144 | NSDIVCEQDIY | 2 | Homo sapiens, Xenopus tropicalis | C144 | NSDIVCEQDIF | 1 | Danio rerio | C30 | PSLLTCGGCQQ | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C33 | LTCGGCQQSIG | 2 | Danio rerio, Xenopus tropicalis | C33 | LTCGGCQQNIG | 1 | Homo sapiens | C54 | YWHEDCLSCDL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C57 | EDCLSCDLCGC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C60 | LSCDLCGCRLG | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | C80 | LGRKLCRRDYL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | D133 | HFCVGDRYLLI | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | D147 | IVCEQDIYEWT | 2 | Homo sapiens, Xenopus tropicalis | D147 | IVCEQDIFEWT | 1 | Danio rerio | D39 | QQNIGDRYFLK | 1 | Homo sapiens | D39 | QQSIGDRFFLK | 1 | Danio rerio | D39 | QQSIGDRYFLK | 1 | Xenopus tropicalis | D83 | KLCRRDYLRLF | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | D91 | RLFGQDGLCAS | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | E105 | RIRAFEMTMRV | 2 | Danio rerio, Xenopus tropicalis | E105 | RIRAYEMTMRV | 1 | Homo sapiens | E145 | SDIVCEQDIYE | 2 | Homo sapiens, Xenopus tropicalis | E145 | SDIVCEQDIFE | 1 | Danio rerio | E52 | DQYWHEDCLSC | 2 | Homo sapiens, Xenopus tropicalis | E52 | EQYWHEDCLSC | 1 | Danio rerio | F120 | YHLECFKCAAC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | F129 | ACQKHFCVGDR | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | F42 | IGDRYFLKAID | 2 | Homo sapiens, Xenopus tropicalis | F42 | IGDRFFLKAIE | 1 | Danio rerio | G132 | KHFCVGDRYLL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | G92 | LFGQDGLCASC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | H51 | IDQYWHEDCLS | 2 | Homo sapiens, Xenopus tropicalis | H51 | IEQYWHEDCLS | 1 | Danio rerio | I101 | SCDKRIRAYEM | 1 | Homo sapiens | I101 | SCEKRIRAFEM | 1 | Danio rerio | I101 | SCDKRIRAFEM | 1 | Xenopus tropicalis | I46 | YFLKAIDQYWH | 2 | Homo sapiens, Xenopus tropicalis | I46 | FFLKAIEQYWH | 1 | Danio rerio | K111 | MTMRVKDKVYH | 2 | Homo sapiens, Xenopus tropicalis | K111 | MTMRVRDKVYH | 1 | Danio rerio | K44 | DRYFLKAIDQY | 2 | Homo sapiens, Xenopus tropicalis | K44 | DRFFLKAIEQY | 1 | Danio rerio | K74 | RRLYYKLGRKL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L117 | DKVYHLECFKC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L136 | VGDRYLLINSD | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L137 | GDRYLLINSDI | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L43 | GDRYFLKAIDQ | 2 | Homo sapiens, Xenopus tropicalis | L43 | GDRFFLKAIEQ | 1 | Danio rerio | L55 | WHEDCLSCDLC | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L64 | LCGCRLGEVGR | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L71 | EVGRRLYYKLG | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | L85 | CRRDYLRLFGQ | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | M106 | IRAYEMTMRVK | 1 | Homo sapiens | M106 | IRAFEMTMRVR | 1 | Danio rerio | M106 | IRAFEMTMRVK | 1 | Xenopus tropicalis | M108 | AYEMTMRVKDK | 1 | Homo sapiens | M108 | AFEMTMRVRDK | 1 | Danio rerio | M108 | AFEMTMRVKDK | 1 | Xenopus tropicalis | Q146 | DIVCEQDIYEW | 2 | Homo sapiens, Xenopus tropicalis | Q146 | DIVCEQDIFEW | 1 | Danio rerio | Q90 | LRLFGQDGLCA | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | R102 | CDKRIRAYEMT | 1 | Homo sapiens | R102 | CEKRIRAFEMT | 1 | Danio rerio | R102 | CDKRIRAFEMT | 1 | Xenopus tropicalis | R109 | YEMTMRVKDKV | 1 | Homo sapiens | R109 | FEMTMRVRDKV | 1 | Danio rerio | R109 | FEMTMRVKDKV | 1 | Xenopus tropicalis | R134 | FCVGDRYLLIN | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | R40 | QNIGDRYFLKA | 1 | Homo sapiens | R40 | QSIGDRFFLKA | 1 | Danio rerio | R40 | QSIGDRYFLKA | 1 | Xenopus tropicalis | R69 | LGEVGRRLYYK | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | R70 | GEVGRRLYYKL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | R81 | GRKLCRRDYLR | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | T107 | RAYEMTMRVKD | 1 | Homo sapiens | T107 | RAFEMTMRVRD | 1 | Danio rerio | T107 | RAFEMTMRVKD | 1 | Xenopus tropicalis | V110 | EMTMRVKDKVY | 2 | Homo sapiens, Xenopus tropicalis | V110 | EMTMRVRDKVY | 1 | Danio rerio | V114 | RVKDKVYHLEC | 2 | Homo sapiens, Xenopus tropicalis | V114 | RVRDKVYHLEC | 1 | Danio rerio | V131 | QKHFCVGDRYL | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | Y104 | KRIRAFEMTMR | 2 | Danio rerio, Xenopus tropicalis | Y104 | KRIRAYEMTMR | 1 | Homo sapiens | Y135 | CVGDRYLLINS | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | Y41 | NIGDRYFLKAI | 1 | Homo sapiens | Y41 | SIGDRFFLKAI | 1 | Danio rerio | Y41 | SIGDRYFLKAI | 1 | Xenopus tropicalis | Y72 | VGRRLYYKLGR | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | Y73 | GRRLYYKLGRK | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis | Y84 | LCRRDYLRLFG | 3 | Homo sapiens, Danio rerio, Xenopus tropicalis |
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