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mutLBSgeneDB |
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| Gene summary for GLYR1 |
 Gene summary |
| Basic gene Info. | Gene symbol | GLYR1 |
| Gene name | glyoxylate reductase 1 homolog (Arabidopsis) | |
| Synonyms | BM045|HIBDL|N-PAC|NP60 | |
| Cytomap | UCSC genome browser: 16p13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_032569.3, | |
| Description | 3-hydroxyisobutyrate dehydrogenase-like proteincytokine-like nuclear factor n-pacnuclear protein 60 kDanuclear protein 60kDanuclear protein NP60nuclear protein of 60 kDaputative oxidoreductase GLYR1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 610660 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000140632 | ||
| HPRD : 17625 | ||
| Vega : OTTHUMG00000129530 | ||
| Protein | UniProt: Q49A26 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_GLYR1 | |
| BioGPS: 84656 | ||
| Pathway | NCI Pathway Interaction Database: GLYR1 | |
| KEGG: GLYR1 | ||
| REACTOME: GLYR1 | ||
| Pathway Commons: GLYR1 | ||
| Context | iHOP: GLYR1 | |
| ligand binding site mutation search in PubMed: GLYR1 | ||
| UCL Cancer Institute: GLYR1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for GLYR1 |
| 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 | R298 | R298S | SKCM | 1 | D339 | K338N | UCEC | 1 | W296 | T294A | 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 GLYR1 |
| 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 | W296 | T294A | -1.1736469 | R298 | R298S | -1.1125888 | D339 | K338N | -0.6552198 |
| (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 GLYR1 from PDB |
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| Differential gene expression and gene-gene network for GLYR1 |
| 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 GLYR1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for GLYR1 |
| 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 GLYR1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NA7 | 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE | 2uyy | A | R298 D339 | NA7 | 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE | 2uyy | D | W296 R298 |
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| Conservation information for LBS of GLYR1 |
| Multiple alignments for Q49A26 in multiple species |
| LBS | AA sequence | # species | Species | A336 | VSDPKAAKDLV | 4 | Homo sapiens, Gallus gallus, Bos taurus, Rattus norvegicus | A336 | VSDPQVAKDMV | 1 | Anopheles gambiae | A336 | LSDPCAALSVV | 1 | Arabidopsis thaliana | A336 | VSDPKAARDLV | 1 | Danio rerio | A336 | VADPKAAKDLV | 1 | Xenopus tropicalis | C330 | DITFACVSDPK | 4 | Homo sapiens, Gallus gallus, Bos taurus, Rattus norvegicus | C330 | DVTYSCVSDPQ | 1 | Anopheles gambiae | C330 | KYTIAMLSDPC | 1 | Arabidopsis thaliana | C330 | DITFSCVSDPK | 1 | Danio rerio | C330 | DITFACVADPK | 1 | Xenopus tropicalis | D339 | PKAAKDLVLGP | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | D339 | PQVAKDMVFGN | 1 | Anopheles gambiae | D339 | PCAALSVVFDK | 1 | Arabidopsis thaliana | D339 | PKAARDLVLGP | 1 | Danio rerio | F498 | NFKPDFYLKYI | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | F498 | EFPTHHALKHM | 1 | Anopheles gambiae | F498 | SYPPAFPLKHQ | 1 | Arabidopsis thaliana | F498 | NFKPDYYLKHI | 1 | Danio rerio | G276 | GFLGLGLMGSG | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | G276 | GFLGLGVMGCG | 1 | Anopheles gambiae | G276 | GFLGLGIMGKA | 1 | Arabidopsis thaliana | K302 | NRTAEKCDLFI | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | K302 | NRSAHKCRKFQ | 1 | Anopheles gambiae | K302 | NRTLSKCDELV | 1 | Arabidopsis thaliana | K505 | LKYIQKDLRLA | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | K505 | LKHMQKDLKLA | 1 | Anopheles gambiae | K505 | LKHQQKDMRLA | 1 | Arabidopsis thaliana | K505 | LKHIQKDLRLA | 1 | Danio rerio | L275 | IGFLGLGLMGS | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | L275 | FGFLGLGVMGC | 1 | Anopheles gambiae | L275 | VGFLGLGIMGK | 1 | Arabidopsis thaliana | L277 | FLGLGLMGSGI | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | L277 | FLGLGVMGCGI | 1 | Anopheles gambiae | L277 | FLGLGIMGKAM | 1 | Arabidopsis thaliana | L277 | FLGLGLMGSGV | 1 | Danio rerio | M278 | LGLGLMGSGIV | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | M278 | LGLGVMGCGIV | 1 | Anopheles gambiae | M278 | LGLGIMGKAMS | 1 | Arabidopsis thaliana | M278 | LGLGLMGSGVV | 1 | Danio rerio | N297 | TVTVWNRTAEK | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | N297 | SVVVWNRSAHK | 1 | Anopheles gambiae | N297 | KVTVWNRTLSK | 1 | Arabidopsis thaliana | N297 | VVTVWNRTAEK | 1 | Danio rerio | R298 | VTVWNRTAEKC | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | R298 | VVVWNRSAHKC | 1 | Anopheles gambiae | R298 | VTVWNRTLSKC | 1 | Arabidopsis thaliana | S332 | TFACVSDPKAA | 4 | Homo sapiens, Gallus gallus, Bos taurus, Rattus norvegicus | S332 | TYSCVSDPQVA | 1 | Anopheles gambiae | S332 | TIAMLSDPCAA | 1 | Arabidopsis thaliana | S332 | TFSCVSDPKAA | 1 | Danio rerio | S332 | TFACVADPKAA | 1 | Xenopus tropicalis | T299 | TVWNRTAEKCD | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | T299 | VVWNRSAHKCR | 1 | Anopheles gambiae | T299 | TVWNRTLSKCD | 1 | Arabidopsis thaliana | T362 | YVDMSTVDADT | 4 | Homo sapiens, Gallus gallus, Bos taurus, Rattus norvegicus | T362 | YVEMTGVDPET | 1 | Anopheles gambiae | T362 | YIDMSTVDAET | 1 | Arabidopsis thaliana | T362 | YVEMSTVDPET | 1 | Danio rerio | T362 | YVDMSTVDPET | 1 | Xenopus tropicalis | V331 | ITFACVSDPKA | 4 | Homo sapiens, Gallus gallus, Bos taurus, Rattus norvegicus | V331 | VTYSCVSDPQV | 1 | Anopheles gambiae | V331 | YTIAMLSDPCA | 1 | Arabidopsis thaliana | V331 | ITFSCVSDPKA | 1 | Danio rerio | V331 | ITFACVADPKA | 1 | Xenopus tropicalis | W296 | HTVTVWNRTAE | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | W296 | HSVVVWNRSAH | 1 | Anopheles gambiae | W296 | FKVTVWNRTLS | 1 | Arabidopsis thaliana | W296 | HVVTVWNRTAE | 1 | Danio rerio | Y499 | FKPDFYLKYIQ | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | Y499 | FPTHHALKHMQ | 1 | Anopheles gambiae | Y499 | YPPAFPLKHQQ | 1 | Arabidopsis thaliana | Y499 | FKPDYYLKHIQ | 1 | Danio rerio | Y502 | DFYLKYIQKDL | 5 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Rattus norvegicus | Y502 | HHALKHMQKDL | 1 | Anopheles gambiae | Y502 | AFPLKHQQKDM | 1 | Arabidopsis thaliana | Y502 | DYYLKHIQKDL | 1 | Danio rerio |
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