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mutLBSgeneDB |
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| Gene summary for PHGDH |
 Gene summary |
| Basic gene Info. | Gene symbol | PHGDH |
| Gene name | phosphoglycerate dehydrogenase | |
| Synonyms | 3-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA | |
| Cytomap | UCSC genome browser: 1p12 | |
| Type of gene | protein-coding | |
| RefGenes | NM_006623.3, | |
| Description | 3-phosphoglycerate dehydrogenaseD-3-phosphoglycerate dehydrogenaseepididymis secretory protein Li 113 | |
| Modification date | 20141211 | |
| dbXrefs | MIM : 606879 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000092621 | ||
| HPRD : 06047 | ||
| Vega : OTTHUMG00000012100 | ||
| Protein | UniProt: O43175 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PHGDH | |
| BioGPS: 26227 | ||
| Pathway | NCI Pathway Interaction Database: PHGDH | |
| KEGG: PHGDH | ||
| REACTOME: PHGDH | ||
| Pathway Commons: PHGDH | ||
| Context | iHOP: PHGDH | |
| ligand binding site mutation search in PubMed: PHGDH | ||
| UCL Cancer Institute: PHGDH | ||
| 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 PHGDH |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | H283 | P282L | SKCM | 1 | A286 | A286V | 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 PHGDH |
| 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 | A286 | A286V | -0.83489312 | H283 | P282L | -0.21063411 |
| (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 PHGDH from PDB |
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| Differential gene expression and gene-gene network for PHGDH |
| 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 PHGDH |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0025202 | Melanoma | 3 | Biomarker |
| umls:C1458155 | Breast Neoplasms | 2 | Biomarker |
| umls:C1866174 | Phosphoglycerate Dehydrogenase Deficiency | 1 | Biomarker, GeneticVariation |
| umls:C0007621 | Cell Transformation, Neoplastic | 1 | Biomarker |
| umls:C0033578 | Prostatic Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PHGDH |
| 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 |
| Nutraceutical | DB00157 | NADH | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PHGDH go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of PHGDH |
| Multiple alignments for O43175 in multiple species |
| LBS | AA sequence | # species | Species | A106 | GNSLSAAELTC | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | A106 | ANTIAAAEHGI | 1 | Arabidopsis thaliana | A235 | RVVNCARGGIV | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | A235 | RIVNVARGGVI | 1 | Arabidopsis thaliana | A235 | CVVNCARGGIV | 1 | Bos taurus | A286 | CPHLGASTKEA | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | A286 | TPHLGASTMEA | 1 | Arabidopsis thaliana | C234 | VRVVNCARGGI | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | C234 | VRIVNVARGGV | 1 | Arabidopsis thaliana | C234 | VCVVNCARGGI | 1 | Bos taurus | D175 | KTIGYDPIISP | 3 | Homo sapiens, Bos taurus, Pan troglodytes | D175 | KTVGYDPIISP | 2 | Mus musculus, Rattus norvegicus | D175 | RVIAHDPYAPA | 1 | Arabidopsis thaliana | D260 | AGAALDVFTEE | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | D260 | AQAALDVFTKE | 1 | Arabidopsis thaliana | G152 | TLGILGLGRIG | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | G152 | TLAVLGFGKVG | 1 | Arabidopsis thaliana | G152 | VLGILGLGRIG | 1 | Bos taurus | G154 | GILGLGRIGRE | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | G154 | AVLGFGKVGTE | 1 | Arabidopsis thaliana | G285 | SCPHLGASTKE | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | G285 | VTPHLGASTME | 1 | Arabidopsis thaliana | H206 | DFITVHTPLLP | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | H206 | DFISLHMPLTP | 1 | Arabidopsis thaliana | H283 | VISCPHLGAST | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | H283 | VTVTPHLGAST | 1 | Arabidopsis thaliana | I156 | LGLGRIGREVA | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | I156 | LGFGKVGTEVA | 1 | Arabidopsis thaliana | N102 | NTPNGNSLSAA | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | N102 | NAPTANTIAAA | 1 | Arabidopsis thaliana | P176 | TIGYDPIISPE | 3 | Homo sapiens, Bos taurus, Pan troglodytes | P176 | TVGYDPIISPE | 2 | Mus musculus, Rattus norvegicus | P176 | VIAHDPYAPAD | 1 | Arabidopsis thaliana | P208 | ITVHTPLLPST | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | P208 | ISLHMPLTPTT | 1 | Arabidopsis thaliana | R155 | ILGLGRIGREV | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | R155 | VLGFGKVGTEV | 1 | Arabidopsis thaliana | R236 | VVNCARGGIVD | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | R236 | IVNVARGGVID | 1 | Arabidopsis thaliana | S212 | TPLLPSTTGLL | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | S212 | MPLTPTTSKIL | 1 | Arabidopsis thaliana | T207 | FITVHTPLLPS | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | T207 | FISLHMPLTPT | 1 | Arabidopsis thaliana | T213 | PLLPSTTGLLN | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | T213 | PLTPTTSKILN | 1 | Arabidopsis thaliana | T78 | VGRAGTGVDNV | 5 | Homo sapiens, Bos taurus, Pan troglodytes, Mus musculus, Rattus norvegicus | T78 | VGRAGVGIDNV | 1 | Arabidopsis thaliana | Y174 | MKTIGYDPIIS | 3 | Homo sapiens, Bos taurus, Pan troglodytes | Y174 | MKTVGYDPIIS | 2 | Mus musculus, Rattus norvegicus | Y174 | MRVIAHDPYAP | 1 | Arabidopsis thaliana |
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