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mutLBSgeneDB |
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| Gene summary for PDXP |
 Gene summary |
| Basic gene Info. | Gene symbol | PDXP |
| Gene name | pyridoxal (pyridoxine, vitamin B6) phosphatase | |
| Synonyms | CIN|PLP|dJ37E16.5 | |
| Cytomap | UCSC genome browser: 22q12.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_020315.4, | |
| Description | PLP phosphatasechronophinpyridoxal phosphate phosphatase | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 609246 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000241360 | ||
| Vega : OTTHUMG00000044618 | ||
| Protein | UniProt: Q96GD0 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PDXP | |
| BioGPS: 57026 | ||
| Pathway | NCI Pathway Interaction Database: PDXP | |
| KEGG: PDXP | ||
| REACTOME: PDXP | ||
| Pathway Commons: PDXP | ||
| Context | iHOP: PDXP | |
| ligand binding site mutation search in PubMed: PDXP | ||
| UCL Cancer Institute: PDXP | ||
| 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 | GO:0006470 | protein dephosphorylation | 15580268 | GO:0031247 | actin rod assembly | 19000834 | GO:0071318 | cellular response to ATP | 19000834 |
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| Ligand binding site mutations for PDXP |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D243 | E241D | BLCA | 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 PDXP |
| 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 | D243 | E241D | -1.1288586 |
| (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 PDXP from PDB |
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| Differential gene expression and gene-gene network for PDXP |
| 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 PDXP |
| 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 PDXP |
| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Nutraceutical | DB00114 | Pyridoxal Phosphate | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PDXP go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 2p69 | A | D243 |
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| Conservation information for LBS of PDXP |
| Multiple alignments for Q96GD0 in multiple species |
| LBS | AA sequence | # species | Species | C26 | GVLFDCDGVLW | 2 | Homo sapiens, Mus musculus | C26 | TFIFDCDGVIW | 2 | Arabidopsis thaliana, Arabidopsis thaliana | C26 | GVLFDCNGVLW | 1 | Bos taurus | D179 | VATDRDPWHPL | 3 | Homo sapiens, Mus musculus, Bos taurus | D179 | IATNRDAVTHL | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D238 | TLMVGDRLETD | 3 | Homo sapiens, Mus musculus, Bos taurus | D238 | ICMVGDRLDTD | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D243 | DRLETDILFGH | 3 | Homo sapiens, Mus musculus, Bos taurus | D243 | DRLDTDILFGQ | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D25 | QGVLFDCDGVL | 2 | Homo sapiens, Mus musculus | D25 | ETFIFDCDGVI | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D25 | QGVLFDCNGVL | 1 | Bos taurus | D27 | VLFDCDGVLWN | 2 | Homo sapiens, Mus musculus | D27 | FIFDCDGVIWK | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D27 | VLFDCNGVLWN | 1 | Bos taurus | H182 | DRDPWHPLSDG | 3 | Homo sapiens, Mus musculus, Bos taurus | H182 | NRDAVTHLTDA | 2 | Arabidopsis thaliana, Arabidopsis thaliana | K213 | ALVVGKPSPYM | 3 | Homo sapiens, Mus musculus, Bos taurus | K213 | PLVVGKPSTFM | 2 | Arabidopsis thaliana, Arabidopsis thaliana | L258 | KTLLVLSGVTS | 2 | Arabidopsis thaliana, Arabidopsis thaliana | L258 | TTVLTLTGVSS | 2 | Mus musculus, Bos taurus | L258 | TTVLTLTGVSR | 1 | Homo sapiens | L264 | SGVTSI----S | 2 | Arabidopsis thaliana, Arabidopsis thaliana | L264 | TGVSSLEEAQA | 2 | Mus musculus, Bos taurus | L264 | TGVSRLEEAQA | 1 | Homo sapiens | N59 | LVFVTNNSTKS | 2 | Arabidopsis thaliana, Arabidopsis thaliana | N59 | TLFVSNNSRRA | 2 | Mus musculus, Bos taurus | N59 | ALFVSNNSRRA | 1 | Homo sapiens | N60 | LFVSNNSRRAR | 3 | Homo sapiens, Mus musculus, Bos taurus | N60 | VFVTNNSTKSR | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R263 | LSGVTSI---- | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R263 | LTGVSSLEEAQ | 2 | Mus musculus, Bos taurus | R263 | LTGVSRLEEAQ | 1 | Homo sapiens | R63 | SNNSRRARPEL | 3 | Homo sapiens, Mus musculus, Bos taurus | R63 | TNNSTKSRKQY | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R71 | PELALRFARLG | 3 | Homo sapiens, Mus musculus, Bos taurus | R71 | KQYGKKFETLG | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R74 | ALRFARLGFGG | 2 | Homo sapiens, Bos taurus | R74 | GKKFETLGL-N | 2 | Arabidopsis thaliana, Arabidopsis thaliana | R74 | ALRFARLGFAG | 1 | Mus musculus | S58 | RLVFVTNNSTK | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S58 | AALFVSNNSRR | 1 | Homo sapiens | S58 | NTLFVSNNSRR | 1 | Mus musculus | S58 | ATLFVSNNSRR | 1 | Bos taurus | Y150 | AVLVGYDEHFS | 2 | Homo sapiens, Bos taurus | Y150 | AVVVGFDRYFN | 2 | Arabidopsis thaliana, Arabidopsis thaliana | Y150 | AVLVGYDEQFS | 1 | Mus musculus |
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