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mutLBSgeneDB |
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| Gene summary for NME3 |
 Gene summary |
| Basic gene Info. | Gene symbol | NME3 |
| Gene name | NME/NM23 nucleoside diphosphate kinase 3 | |
| Synonyms | DR-nm23|NDPK-C|NDPKC|NM23-H3|NM23H3|c371H6.2 | |
| Cytomap | UCSC genome browser: 16q13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002513.2, | |
| Description | NDK 3NDP kinase 3NDP kinase Cnon-metastatic cells 3, protein expressed innucleoside diphosphate kinase 3nucleoside diphosphate kinase C | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601817 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000103024 | ||
| HPRD : 03488 | ||
| Vega : OTTHUMG00000128635 | ||
| Protein | UniProt: Q13232 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NME3 | |
| BioGPS: 4832 | ||
| Pathway | NCI Pathway Interaction Database: NME3 | |
| KEGG: NME3 | ||
| REACTOME: NME3 | ||
| Pathway Commons: NME3 | ||
| Context | iHOP: NME3 | |
| ligand binding site mutation search in PubMed: NME3 | ||
| UCL Cancer Institute: NME3 | ||
| 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 NME3 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R122 | D124Y | COAD | 1 | R122 | R122H | LUSC | 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 NME3 |
| 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 | R122 | R122H | -1.1124381 | R122 | D124Y | -0.98918891 |
| (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 NME3 from PDB |
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| Differential gene expression and gene-gene network for NME3 |
| 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 NME3 |
| 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 NME3 |
| 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 NME3 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ADP | ADP | 1zs6 | A | R122 |
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| Conservation information for LBS of NME3 |
| Multiple alignments for Q13232 in multiple species |
| LBS | AA sequence | # species | Species | F77 | LRERPFYGRLV | 1 | Homo sapiens | F77 | LSAKSFFPNLI | 1 | Arabidopsis thaliana | F77 | LREKPFYSRLV | 1 | Mus musculus | G130 | FCIEVGKNLIH | 1 | Homo sapiens | G130 | LAVQTGRNIVH | 1 | Arabidopsis thaliana | G130 | FCMEVGKNVIH | 1 | Mus musculus | K29 | TFLAVKPDGVQ | 2 | Homo sapiens, Mus musculus | K29 | TYIMVKPDGIQ | 1 | Arabidopsis thaliana | L72 | EHYAELRERPF | 1 | Homo sapiens | L72 | EHYKDLSAKSF | 1 | Arabidopsis thaliana | L72 | EHYVELREKPF | 1 | Mus musculus | L81 | PFYGRLVKYMA | 1 | Homo sapiens | L81 | SFFPNLIEYIT | 1 | Arabidopsis thaliana | L81 | PFYSRLVKYMS | 1 | Mus musculus | N132 | IEVGKNLIHGS | 1 | Homo sapiens | N132 | VQTGRNIVHGS | 1 | Arabidopsis thaliana | N132 | MEVGKNVIHGS | 1 | Mus musculus | R105 | VVRTSRALIGA | 1 | Homo sapiens | R105 | VVASARKLIGK | 1 | Arabidopsis thaliana | R105 | VVHASRALIGA | 1 | Mus musculus | R122 | PPGTIRGDFCI | 1 | Homo sapiens | R122 | EPGTIRGDLAV | 1 | Arabidopsis thaliana | R122 | MPGTIRGDFCM | 1 | Mus musculus | T111 | ALIGATNPADA | 1 | Homo sapiens | T111 | KLIGKTDPLQA | 1 | Arabidopsis thaliana | T111 | ALIGATDPGDA | 1 | Mus musculus | V129 | DFCIEVGKNLI | 1 | Homo sapiens | V129 | DLAVQTGRNIV | 1 | Arabidopsis thaliana | V129 | DFCMEVGKNVI | 1 | Mus musculus | Y69 | LLREHYAELRE | 1 | Homo sapiens | Y69 | LAEEHYKDLSA | 1 | Arabidopsis thaliana | Y69 | LLREHYVELRE | 1 | Mus musculus |
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