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mutLBSgeneDB |
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| Gene summary for PGAM1 |
 Gene summary |
| Basic gene Info. | Gene symbol | PGAM1 |
| Gene name | phosphoglycerate mutase 1 (brain) | |
| Synonyms | HEL-S-35|PGAM-B|PGAMA | |
| Cytomap | UCSC genome browser: 10q25.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002629.2, | |
| Description | BPG-dependent PGAM 1epididymis secretory protein Li 35phosphoglycerate mutase 1phosphoglycerate mutase A, nonmuscle formphosphoglycerate mutase isozyme B | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 172250 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000171314 | ||
| HPRD : 01392 | ||
| Vega : OTTHUMG00000018846 | ||
| Protein | UniProt: P18669 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PGAM1 | |
| BioGPS: 5223 | ||
| Pathway | NCI Pathway Interaction Database: PGAM1 | |
| KEGG: PGAM1 | ||
| REACTOME: PGAM1 | ||
| Pathway Commons: PGAM1 | ||
| Context | iHOP: PGAM1 | |
| ligand binding site mutation search in PubMed: PGAM1 | ||
| UCL Cancer Institute: PGAM1 | ||
| 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:0006096 | glycolytic process | 22590500 | GO:0006110 | regulation of glycolytic process | 12189148 | GO:0043456 | regulation of pentose-phosphate shunt | 12189148 | GO:0045730 | respiratory burst | 12189148 |
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| Ligand binding site mutations for PGAM1 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R62 | A63V | COAD | 1 | R10 | L8V | KIRC | 1 | E89 | R90W | 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 PGAM1 |
| 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 | E89 | R90W | -1.3979534 | R10 | L8V | -0.80232314 | R62 | A63V | -0.447345 |
| (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 PGAM1 from PDB |
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| Differential gene expression and gene-gene network for PGAM1 |
| 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 PGAM1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0001418 | Adenocarcinoma | 1 | Biomarker |
| umls:C0007097 | Carcinoma | 1 | Biomarker |
| umls:C0007131 | Carcinoma, Non-Small-Cell Lung | 1 | Biomarker |
| umls:C0007137 | Carcinoma, Squamous Cell | 1 | Biomarker |
| umls:C0024667 | Mammary Neoplasms, Animal | 1 | Biomarker |
| umls:C0024668 | Mammary Neoplasms, Experimental | 1 | Biomarker |
| umls:C0026640 | Mouth Neoplasms | 1 | Biomarker |
| umls:C0038356 | Stomach 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 PGAM1 |
| 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 PGAM1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CIT | CITRIC ACID | 1yfk | A | E89 | CIT | CITRIC ACID | 1yjx | B | E89 | CIT | CITRIC ACID | 1yjx | C | E89 | CIT | CITRIC ACID | 1yjx | D | E89 | CIT | CITRIC ACID | 1yjx | E | E89 | CIT | CITRIC ACID | 1yjx | F | R10 E89 | CIT | CITRIC ACID | 1yjx | I | R10 E89 | CIT | CITRIC ACID | 1yjx | K | R10 E89 | CIT | CITRIC ACID | 1yjx | H | R62 | CIT | CITRIC ACID | 1yfk | B | R62 E89 |
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| Conservation information for LBS of PGAM1 |
| Multiple alignments for P18669 in multiple species |
| LBS | AA sequence | # species | Species | E89 | TWRLNERHYGG | 3 | Homo sapiens, Bos taurus, Mus musculus | E89 | TWRLNERHYGA | 1 | Gallus gallus | F22 | NLENRFSGWYD | 3 | Homo sapiens, Bos taurus, Mus musculus | F22 | NLENRFCGWYD | 1 | Gallus gallus | G24 | ENRFSGWYDAD | 3 | Homo sapiens, Bos taurus, Mus musculus | G24 | ENRFCGWYDAD | 1 | Gallus gallus | K100 | LTGLNKAETAA | 4 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus | N17 | GESAWNLENRF | 3 | Homo sapiens, Gallus gallus, Mus musculus | N17 | GESTWNLENRF | 1 | Bos taurus | R10 | KLVLIRHGESA | 2 | Homo sapiens, Mus musculus | R10 | RLVLVRHGESA | 1 | Gallus gallus | R10 | KLVLIRHGEST | 1 | Bos taurus | R116 | QVKIWRRSYDV | 3 | Homo sapiens, Bos taurus, Mus musculus | R116 | QVKIWRRSFDI | 1 | Gallus gallus | R21 | WNLENRFSGWY | 3 | Homo sapiens, Bos taurus, Mus musculus | R21 | WNLENRFCGWY | 1 | Gallus gallus | R62 | TSVQKRAIRTL | 4 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus | R83 | WLPVVRTWRLN | 4 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus | S23 | LENRFSGWYDA | 3 | Homo sapiens, Bos taurus, Mus musculus | S23 | LENRFCGWYDA | 1 | Gallus gallus | V81 | QMWLPVVRTWR | 4 | Homo sapiens, Gallus gallus, Bos taurus, Mus musculus | W68 | AIRTLWTVLDA | 3 | Homo sapiens, Bos taurus, Mus musculus | W68 | AIRTLWNVLDA | 1 | Gallus gallus | Y92 | LNERHYGGLTG | 3 | Homo sapiens, Bos taurus, Mus musculus | Y92 | LNERHYGALTG | 1 | Gallus gallus |
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