|
mutLBSgeneDB |
| |
| |
| |
| |
| |
| |
|
| Gene summary for GNPDA1 |
 Gene summary |
| Basic gene Info. | Gene symbol | GNPDA1 |
| Gene name | glucosamine-6-phosphate deaminase 1 | |
| Synonyms | GNP1|GNPDA|GNPI|GPI|HLN | |
| Cytomap | UCSC genome browser: 5q21 | |
| Type of gene | protein-coding | |
| RefGenes | NM_005471.4, | |
| Description | GNPDA 1glcN6P deaminase 1glucosamine-6-phosphate isomerase 1oscillin | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601798 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000113552 | ||
| HPRD : 09048 | ||
| Vega : OTTHUMG00000129657 | ||
| Protein | UniProt: P46926 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_GNPDA1 | |
| BioGPS: 10007 | ||
| Pathway | NCI Pathway Interaction Database: GNPDA1 | |
| KEGG: GNPDA1 | ||
| REACTOME: GNPDA1 | ||
| Pathway Commons: GNPDA1 | ||
| Context | iHOP: GNPDA1 | |
| ligand binding site mutation search in PubMed: GNPDA1 | ||
| UCL Cancer Institute: GNPDA1 | ||
| 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 |
| Top |
| Ligand binding site mutations for GNPDA1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G137 | G136A | HNSC | 1 | P40 | L39H | KIRC | 1 | G139 | G139C | LUAD | 1 | R158 | R158C | STAD | 1 | K33 | E32D | 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. |
| Top |
| Protein structure related information for GNPDA1 |
| 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 | P40 | L39H | -1.8929209 | R158 | R158C | -1.1199152 | K33 | E32D | -0.45893086 | G137 | G136A | -0.33897854 | G139 | G139C | -0.25006871 |
| (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 GNPDA1 from PDB |
| Top |
| Differential gene expression and gene-gene network for GNPDA1 |
| 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) |
| Top |
| Top |
| Phenotype information for GNPDA1 |
| 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 |
| Top |
| Pharmacological information for GNPDA1 |
| 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. |
 |
| Gene-centered drug-gene interaction network |
 |
| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB02379 | Beta-D-Glucose | Small molecule |  |
| Experimental | DB02445 | 2-Deoxy-2-Amino Glucitol-6-Phosphate | Small molecule |  |
| Experimental | DB03951 | 16g | Small molecule |  |
| Gene-centered ligand-gene interaction network |
 |
| Ligands binding to mutated ligand binding site of GNPDA1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | AGP | 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE | 1ne7 | B | G137 | AGP | 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE | 1ne7 | E | G137 | AGP | 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE | 1ne7 | D | G137 G139 | GLC | ALPHA-D-GLUCOSE | 1ne7 | A | K33 | GLC | ALPHA-D-GLUCOSE | 1ne7 | B | K33 | GLC | ALPHA-D-GLUCOSE | 1ne7 | C | K33 | GLC | ALPHA-D-GLUCOSE | 1ne7 | D | K33 | GLC | ALPHA-D-GLUCOSE | 1ne7 | E | K33 | GLC | ALPHA-D-GLUCOSE | 1ne7 | F | K33 | AGP | 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE | 1ne7 | A | P40 G137 | AGP | 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE | 1ne7 | F | P40 G137 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | A | R158 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | B | R158 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | C | R158 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | D | R158 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | E | R158 | 16G | 2-ACETAMIDO-2-DEOXY-6-O-PHOSPHONOHEXOPYRANOSE | 1ne7 | F | R158 |
| Top |
| Conservation information for LBS of GNPDA1 |
| Multiple alignments for P46926 in multiple species |
| LBS | AA sequence | # species | Species | A145 | PDGHIAFNEPG | 3 | Homo sapiens, Mus musculus, Bos taurus | D72 | KTFNMDEYVGL | 3 | Homo sapiens, Mus musculus, Bos taurus | F146 | DGHIAFNEPGS | 3 | Homo sapiens, Mus musculus, Bos taurus | F27 | NRIIQFNPGPD | 2 | Mus musculus, Bos taurus | F27 | NRIIQFNPGPE | 1 | Homo sapiens | G137 | ELFVGGIGPDG | 3 | Homo sapiens, Mus musculus, Bos taurus | G139 | FVGGIGPDGHI | 3 | Homo sapiens, Mus musculus, Bos taurus | G42 | LGLPTGSTPLG | 3 | Homo sapiens, Mus musculus, Bos taurus | H143 | IGPDGHIAFNE | 3 | Homo sapiens, Mus musculus, Bos taurus | H262 | GLMLVHNKLVD | 3 | Homo sapiens, Mus musculus, Bos taurus | I138 | LFVGGIGPDGH | 3 | Homo sapiens, Mus musculus, Bos taurus | K160 | SRTRVKTLAMD | 3 | Homo sapiens, Mus musculus, Bos taurus | K2 | 3 | Homo sapiens, Mus musculus, Bos taurus | K208 | ITGAHKAFALY | 3 | Homo sapiens, Mus musculus, Bos taurus | K33 | NPGPDKYFTLG | 2 | Mus musculus, Bos taurus | K33 | NPGPEKYFTLG | 1 | Homo sapiens | M1 | 3 | Homo sapiens, Mus musculus, Bos taurus | M184 | AKVPTMALTVG | 2 | Mus musculus, Bos taurus | M184 | TKVPTMALTVG | 1 | Homo sapiens | M71 | VKTFNMDEYVG | 3 | Homo sapiens, Mus musculus, Bos taurus | N170 | DTILANARFFD | 3 | Homo sapiens, Mus musculus, Bos taurus | P40 | FTLGLPTGSTP | 3 | Homo sapiens, Mus musculus, Bos taurus | P45 | PTGSTPLGCYK | 2 | Homo sapiens, Bos taurus | P45 | PTGSTPLGCYQ | 1 | Mus musculus | R158 | LVSRTRVKTLA | 3 | Homo sapiens, Mus musculus, Bos taurus | R172 | ILANARFFDGD | 2 | Mus musculus, Bos taurus | R172 | ILANARFFDGE | 1 | Homo sapiens | S151 | FNEPGSSLVSR | 3 | Homo sapiens, Mus musculus, Bos taurus | S152 | NEPGSSLVSRT | 3 | Homo sapiens, Mus musculus, Bos taurus | S43 | GLPTGSTPLGC | 3 | Homo sapiens, Mus musculus, Bos taurus | T161 | RTRVKTLAMDT | 3 | Homo sapiens, Mus musculus, Bos taurus | T166 | TLAMDTILANA | 3 | Homo sapiens, Mus musculus, Bos taurus | T41 | TLGLPTGSTPL | 3 | Homo sapiens, Mus musculus, Bos taurus | T44 | LPTGSTPLGCY | 3 | Homo sapiens, Mus musculus, Bos taurus | V159 | VSRTRVKTLAM | 3 | Homo sapiens, Mus musculus, Bos taurus | Y85 | DHPESYHSFMW | 3 | Homo sapiens, Mus musculus, Bos taurus |
 |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |