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mutLBSgeneDB |
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| Gene summary for PSPH |
 Gene summary |
| Basic gene Info. | Gene symbol | PSPH |
| Gene name | phosphoserine phosphatase | |
| Synonyms | PSP|PSPHD | |
| Cytomap | UCSC genome browser: 7p11.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_004577.3, | |
| Description | L-3-phosphoserine phosphataseO-phosphoserine phosphohydrolasePSPase | |
| Modification date | 20141211 | |
| dbXrefs | MIM : 172480 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000146733 | ||
| HPRD : 01406 | ||
| Vega : OTTHUMG00000023441 | ||
| Protein | UniProt: P78330 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PSPH | |
| BioGPS: 5723 | ||
| Pathway | NCI Pathway Interaction Database: PSPH | |
| KEGG: PSPH | ||
| REACTOME: PSPH | ||
| Pathway Commons: PSPH | ||
| Context | iHOP: PSPH | |
| ligand binding site mutation search in PubMed: PSPH | ||
| UCL Cancer Institute: PSPH | ||
| 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:0006563 | L-serine metabolic process | 15291819 | GO:0016311 | dephosphorylation | 14673469 |
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| Ligand binding site mutations for PSPH |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D20 | C18F | BLCA | 1 | E29 | R27T | GBM | 1 | P189 | D191H | SKCM | 1 | P189 | P189S | SKCM | 1 | P189 | D191H | 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 PSPH |
| 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 | P189 | D191H | -1.3000927 | E29 | R27T | -0.82087296 | P189 | P189S | -0.2907248 | D20 | C18F | -0.235392 |
| (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 PSPH from PDB |
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| Differential gene expression and gene-gene network for PSPH |
| 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 PSPH |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1291463 | Deficiency of phosphoserine phosphatase | 1 | GeneticVariation |
| umls:C0002514 | Amino Acid Metabolism, Inborn Errors | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PSPH |
| 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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| 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 |
| Experimental | DB03292 | D-2-Amino-3-Phosphono-Propionic Acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PSPH go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | APO | PROPANOIC ACID | 1l8l | B | D20 | PO4 | PHOSPHATE ION | 1l8o | A | D20 | PO4 | PHOSPHATE ION | 1l8o | B | D20 | CA | CALCIUM(2+) | 1nnl | A | D20 | CA | CALCIUM(2+) | 1nnl | B | D20 | APO | PROPANOIC ACID | 1l8l | A | D20 E29 | CA | CALCIUM(2+) | 1nnl | B | P189 |
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| Conservation information for LBS of PSPH |
| Multiple alignments for P78330 in multiple species |
| LBS | AA sequence | # species | Species | A181 | MIGDGATDMEA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A181 | MIGDGATDLEA | 2 | Drosophila melanogaster, Arabidopsis thaliana | A181 | MVGDGATDMEA | 1 | Bos taurus | D179 | I-MIGDGATDM | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D179 | ITMIGDGATDL | 1 | Drosophila melanogaster | D179 | A-MIGDGATDL | 1 | Arabidopsis thaliana | D179 | V-MVGDGATDM | 1 | Bos taurus | D183 | GDGATDMEACP | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D183 | GDGATDLEAVP | 1 | Drosophila melanogaster | D183 | GDGATDLEARK | 1 | Arabidopsis thaliana | D20 | DAVCFDVDSTV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D20 | QIVCFDVDSTV | 1 | Drosophila melanogaster | D20 | EAVCFDVDSTV | 1 | Arabidopsis thaliana | D22 | VCFDVDSTVIR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D22 | VCFDVDSTVIC | 1 | Drosophila melanogaster | D22 | VCFDVDSTVCV | 1 | Arabidopsis thaliana | D22 | VCFDVDSTVIQ | 1 | Bos taurus | E185 | GATDMEACPP- | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E185 | GATDLEAVPP- | 1 | Drosophila melanogaster | E185 | GATDLEARKPG | 1 | Arabidopsis thaliana | E29 | TVIREEGIDEL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E29 | TVICEEGIDEL | 1 | Drosophila melanogaster | E29 | TVCVDEGIDEL | 1 | Arabidopsis thaliana | E29 | TVIQEEGIDEL | 1 | Bos taurus | G110 | VFLISGGFRSI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G110 | VYLISGGFDCL | 1 | Drosophila melanogaster | G110 | VYLISGGFRQM | 1 | Arabidopsis thaliana | G111 | FLISGGFRSIV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G111 | YLISGGFDCLI | 1 | Drosophila melanogaster | G111 | YLISGGFRQMI | 1 | Arabidopsis thaliana | G180 | -MIGDGATDME | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G180 | TMIGDGATDLE | 1 | Drosophila melanogaster | G180 | -MIGDGATDLE | 1 | Arabidopsis thaliana | G180 | -MVGDGATDME | 1 | Bos taurus | K158 | AESGGKGKVIK | 2 | Homo sapiens, Bos taurus | K158 | SRSGGKAEAIA | 1 | Drosophila melanogaster | K158 | SRSGGKAKAVQ | 1 | Arabidopsis thaliana | K158 | AESGGKGKVIR | 1 | Mus musculus | K158 | AESGGKGKVIG | 1 | Rattus norvegicus | P188 | DMEACPP--AD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | P188 | DLEAVPP--AN | 1 | Drosophila melanogaster | P188 | DLEARKPGGAD | 1 | Arabidopsis thaliana | P189 | MEACPP--ADA | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | P189 | LEAVPP--ANY | 1 | Drosophila melanogaster | P189 | LEARKPGGADL | 1 | Arabidopsis thaliana | R202 | GGNVIRQQVKD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | R202 | GGNVVRPEVYR | 1 | Drosophila melanogaster | R202 | AGVQLREAVAA | 1 | Arabidopsis thaliana | S109 | QVFLISGGFRS | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | S109 | QVYLISGGFDC | 1 | Drosophila melanogaster | S109 | DVYLISGGFRQ | 1 | Arabidopsis thaliana | T182 | IGDGATDMEAC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T182 | IGDGATDLEAV | 1 | Drosophila melanogaster | T182 | IGDGATDLEAR | 1 | Arabidopsis thaliana | T182 | VGDGATDMEAC | 1 | Bos taurus | V21 | AVCFDVDSTVI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | V21 | IVCFDVDSTVI | 1 | Drosophila melanogaster | V21 | AVCFDVDSTVC | 1 | Arabidopsis thaliana |
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