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mutLBSgeneDB |
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| Gene summary for CPS1 |
 Gene summary |
| Basic gene Info. | Gene symbol | CPS1 |
| Gene name | carbamoyl-phosphate synthase 1, mitochondrial | |
| Synonyms | CPSASE1|PHN | |
| Cytomap | UCSC genome browser: 2q35 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001122633.2, NM_001122634.2,NM_001875.4, | |
| Description | carbamoyl-phosphate synthase [ammonia], mitochondrialcarbamoylphosphate synthetase I | |
| Modification date | 20141211 | |
| dbXrefs | MIM : 608307 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000021826 | ||
| HPRD : 01995 | ||
| Vega : OTTHUMG00000132994 | ||
| Protein | UniProt: P31327 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_CPS1 | |
| BioGPS: 1373 | ||
| Pathway | NCI Pathway Interaction Database: CPS1 | |
| KEGG: CPS1 | ||
| REACTOME: CPS1 | ||
| Pathway Commons: CPS1 | ||
| Context | iHOP: CPS1 | |
| ligand binding site mutation search in PubMed: CPS1 | ||
| UCL Cancer Institute: CPS1 | ||
| 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:0032496 | response to lipopolysaccharide | 15897806 | GO:0050667 | homocysteine metabolic process | 20031578 |
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| Ligand binding site mutations for CPS1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | S1203 | S1203P | COAD | 2 | I713 | I713S | BRCA | 1 | E631 | E631Q | GBM | 1 | V1170 | E1171Q | HNSC | 1 | L1245 | V1246A | KIRC | 1 | F1445,N1449 | H1447D | LUAD | 1 | M656 | M656K | LUSC | 1 | M656 | M656I | LUSC | 1 | E623 | V622L | LUSC | 1 | T1443 | T1443A | LUSC | 1 | F1445,N1449 | H1447Y | SKCM | 1 | S625 | S625P | STAD | 1 | R547 | Q548P | STAD | 1 | R587 | R587H | STAD | 1 | L1245 | L1245I | 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. |
| Clinical information for CPS1 from My Cancer Genome. |
| Carbamoyl-phosphate synthase 1, mitochondrial (CPS1) is a gene that encodes a protein that catalyzes the synthesis of carbamoyl phosphate from ammonia and bicarbonate. The protein may also function as a core mitochondrial nucleoid protein. Missense mutations, nonsense mutations, silent mutations, and frameshift insertions and deletions are observed in cancers such as intestinal cancer, lung cancer, and peritoneal cancer. Modified: July 1, 2015 |
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| Protein structure related information for CPS1 |
| Protein structure of wild type (WT) and mutant type (MT) of CPS1 |
| Wild type CPS1 |
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| Mutant type CPS1 |
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| Free energy of binding of drugs to wild type and mutant tpye of CPS1 |
| Gene symbol | Drug name | Free energy of binding (kcal/mol) of wild type | Free energy of binding (kcal/mol) of mutant type | CPS1 | Carglumic Acid | -6.4 | -6.3 |
| 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 | S1203 | S1203P | 0.16082155 | L1245 | V1246A | -1.810993 | T1443 | T1443A | -1.659284 | M656 | M656K | -1.4427946 | R587 | R587H | -1.431159 | I713 | I713S | -1.3251927 | L1245 | L1245I | -1.1819803 | M656 | M656I | -1.0206462 | R547 | Q548P | -1.0059304 | E623 | V622L | -0.94907776 | N1449 | H1447D | -0.81580977 | F1445 | H1447D | -0.81580977 | E631 | E631Q | -0.74755935 | S625 | S625P | -0.73274628 | V1170 | E1171Q | -0.63804434 | F1445 | H1447Y | -0.57029005 | N1449 | H1447Y | -0.57029005 |
| (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 CPS1 from PDB |
| PDB ID | PDB title | PDB structure | 2YVQ | Crystal structure of MGS domain of carbamoyl-phosphate synthetase from homo sapiens |  |
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| Differential gene expression and gene-gene network for CPS1 |
| 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 CPS1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0751753 | Carbamoyl-Phosphate Synthase I Deficiency Disease | 11 | Biomarker, GeneticVariation |
| umls:C0220994 | Hyperammonemia | 3 | Biomarker, GeneticVariation |
| umls:C0023893 | Liver Cirrhosis, Experimental | 2 | Biomarker |
| umls:C0376618 | Endotoxemia | 1 | Biomarker |
| umls:C0031190 | Persistent Fetal Circulation Syndrome | 1 | Biomarker |
| umls:C0032927 | Precancerous Conditions | 1 | Biomarker |
| umls:C0032768 | Neuralgia, Postherpetic | 1 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for CPS1 |
| 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 |
| Approved | DB06775 | Carglumic Acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of CPS1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ADP | ADP | 5dou | A | R547 R587 E623 S625 E631 M656 I713 | ADP | ADP | 5dou | B | R547 R587 E623 S625 E631 M656 I713 | ADP | ADP | 5dou | C | R547 R587 E623 S625 E631 M656 I713 | ADP | ADP | 5dou | D | R547 R587 E623 S625 E631 M656 I713 | NLG | N-ACETYL-L-GLUTAMATE(2-) | 5dou | A | T1443 F1445 N1449 | NLG | N-ACETYL-L-GLUTAMATE(2-) | 5dou | B | T1443 F1445 N1449 | NLG | N-ACETYL-L-GLUTAMATE(2-) | 5dou | C | T1443 F1445 N1449 | NLG | N-ACETYL-L-GLUTAMATE(2-) | 5dou | D | T1443 F1445 N1449 | ADP | ADP | 5dou | A | V1170 S1203 L1245 | ADP | ADP | 5dou | B | V1170 S1203 L1245 | ADP | ADP | 5dou | C | V1170 S1203 L1245 | ADP | ADP | 5dou | D | V1170 S1203 L1245 |
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| Conservation information for LBS of CPS1 |
| Multiple alignments for P31327 in multiple species |
| LBS | AA sequence | # species | Species | A1104 | LKVAQAPWKAV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A1104 | LKIEQPKGGIA | 1 | Arabidopsis thaliana | A1104 | LGIEQPKGGIA | 1 | Oryza sativa subsp. japonica | A1199 | EHVEDAGVHSG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A1199 | EHIEQAGVHSG | 1 | Arabidopsis thaliana | A1199 | EHIEQAGIHSG | 1 | Oryza sativa subsp. japonica | A1393 | LFATEATSDWL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A1393 | IVATSGTAHFL | 1 | Arabidopsis thaliana | A1393 | IIATSGTAKVL | 1 | Oryza sativa subsp. japonica | A591 | IRSAYALGGLG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | A591 | IRPAFTLGGTG | 1 | Arabidopsis thaliana | A591 | VRPAFTLGGTG | 1 | Oryza sativa subsp. japonica | E1175 | VEGAREVEMDA | 2 | Homo sapiens, Mus musculus | E1175 | IEGAREVEMDA | 1 | Rattus norvegicus | E1175 | LSDAIEIDVDT | 1 | Arabidopsis thaliana | E1175 | LIDAIEIDVDA | 1 | Oryza sativa subsp. japonica | E1255 | DVLVIECNLRA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E1255 | DVFLLEANPRA | 1 | Arabidopsis thaliana | E1255 | EVFLLEANPRA | 1 | Oryza sativa subsp. japonica | E623 | NQILVERSVTG | 2 | Mus musculus, Rattus norvegicus | E623 | NQILVEKSVTG | 1 | Homo sapiens | E623 | SQVLVEKSLLG | 1 | Arabidopsis thaliana | E623 | QQVLVEKSLLG | 1 | Oryza sativa subsp. japonica | E631 | VTGWKEIEYEV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E631 | LLGWKEYELEV | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | E714 | EYCIIEVNARL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E714 | EVMIIEMNPRV | 1 | Arabidopsis thaliana | E714 | EVMVIEMNPRV | 1 | Oryza sativa subsp. japonica | F1169 | VVLTKFVEGAR | 2 | Homo sapiens, Mus musculus | F1169 | VVLTKFIEGAR | 1 | Rattus norvegicus | F1169 | VLVDKYLSDAI | 1 | Arabidopsis thaliana | F1169 | VLVDKYLIDAI | 1 | Oryza sativa subsp. japonica | F1445 | NNNTKFVHDNY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F1445 | SGDALDQKDGR | 1 | Arabidopsis thaliana | F1445 | SGDALDSKDGL | 1 | Oryza sativa subsp. japonica | G1200 | HVEDAGVHSGD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G1200 | HIEQAGVHSGD | 1 | Arabidopsis thaliana | G1200 | HIEQAGIHSGD | 1 | Oryza sativa subsp. japonica | G593 | SAYALGGLGSG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G593 | PAFTLGGTGGG | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | G594 | AYALGGLGSGI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G594 | AFTLGGTGGGI | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | G657 | NVDAMGVHTGD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G657 | NIDPMGVHTGD | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | H1202 | EDAGVHSGDAT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H1202 | EQAGVHSGDSA | 1 | Arabidopsis thaliana | H1202 | EQAGIHSGDSA | 1 | Oryza sativa subsp. japonica | H659 | DAMGVHTGDSV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H659 | DPMGVHTGDSI | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | I1254 | NDVLVIECNLR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I1254 | GDVFLLEANPR | 1 | Arabidopsis thaliana | I1254 | GEVFLLEANPR | 1 | Oryza sativa subsp. japonica | I1366 | -ILIGIQQSFR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I1366 | TVFLSLNDMTK | 1 | Arabidopsis thaliana | I1366 | TVFLSLNDLTK | 1 | Oryza sativa subsp. japonica | I713 | MEYCIIEVNAR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I713 | GEVMIIEMNPR | 1 | Arabidopsis thaliana | I713 | GEVMVIEMNPR | 1 | Oryza sativa subsp. japonica | K1168 | PVVLTKFVEGA | 2 | Homo sapiens, Mus musculus | K1168 | PVVLTKFIEGA | 1 | Rattus norvegicus | K1168 | PVLVDKYLSDA | 1 | Arabidopsis thaliana | K1168 | PVLVDKYLIDA | 1 | Oryza sativa subsp. japonica | K1444 | PNNNTKFVHDN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K1444 | SSGDALDQKDG | 1 | Arabidopsis thaliana | K1444 | SSGDALDSKDG | 1 | Oryza sativa subsp. japonica | K624 | QILVERSVTGW | 2 | Mus musculus, Rattus norvegicus | K624 | QVLVEKSLLGW | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | K624 | QILVEKSVTGW | 1 | Homo sapiens | L1245 | NVQF-LVKGND | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L1245 | NCQYAITTSGD | 1 | Arabidopsis thaliana | L1245 | NCQYAITTSGE | 1 | Oryza sativa subsp. japonica | L1438 | DLVINLPNNNT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L1438 | HLMLITSSGDA | 1 | Arabidopsis thaliana | L1438 | QVMVITSSGDA | 1 | Oryza sativa subsp. japonica | L592 | RSAYALGGLGS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L592 | RPAFTLGGTGG | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | M1139 | LSGSAMNVVFS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M1139 | LGGRAMEIVYD | 1 | Arabidopsis thaliana | M1139 | LGGRAMEIVYN | 1 | Oryza sativa subsp. japonica | M585 | G-YPVMIRSAY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M585 | GEFPLIIRPAF | 1 | Arabidopsis thaliana | M585 | GEFPLIVRPAF | 1 | Oryza sativa subsp. japonica | M656 | ENVDAMGVHTG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M656 | ENIDPMGVHTG | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | N1449 | KFVHDNYVIRR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N1449 | LDQKDGRQLRQ | 1 | Arabidopsis thaliana | N1449 | LDSKDGLQLRR | 1 | Oryza sativa subsp. japonica | N716 | CIIEVNARLSR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N716 | MIIEMNPRVSR | 1 | Arabidopsis thaliana | N716 | MVIEMNPRVSR | 1 | Oryza sativa subsp. japonica | P1439 | LVINLPNNNTK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P1439 | LMLITSSGDAL | 1 | Arabidopsis thaliana | P1439 | VMVITSSGDAL | 1 | Oryza sativa subsp. japonica | Q1243 | GPFNVQF-LVK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q1243 | GLMNCQYAITT | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | Q1367 | ILIGIQQSFRP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q1367 | VFLSLNDMTKP | 1 | Arabidopsis thaliana | Q1367 | VFLSLNDLTKR | 1 | Oryza sativa subsp. japonica | Q700 | GECNIQFALHP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q700 | GGSNVQFAVNP | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | R547 | MATEDRQLFSD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R547 | KKAEDRELFKD | 1 | Arabidopsis thaliana | R547 | RAAEDRQLFKQ | 1 | Oryza sativa subsp. japonica | R587 | YPVMIRSAYAL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R587 | FPLIIRPAFTL | 1 | Arabidopsis thaliana | R587 | FPLIVRPAFTL | 1 | Oryza sativa subsp. japonica | R718 | IEVNARLSRSS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R718 | IEMNPRVSRSS | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | R721 | NARLSRSSALA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R721 | NPRVSRSSALA | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | S1203 | DAGVHSGDATL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S1203 | QAGVHSGDSAC | 1 | Arabidopsis thaliana | S1203 | QAGIHSGDSAC | 1 | Oryza sativa subsp. japonica | S625 | ILVERSVTGWK | 2 | Mus musculus, Rattus norvegicus | S625 | VLVEKSLLGWK | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | S625 | ILVEKSVTGWK | 1 | Homo sapiens | S790 | SSRIGSSMKSV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S790 | QPLLTTQMKSV | 1 | Arabidopsis thaliana | S790 | EPVLTTQMKSV | 1 | Oryza sativa subsp. japonica | T1391 | FKLFATEATSD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T1391 | FKIVATSGTAH | 1 | Arabidopsis thaliana | T1391 | FNIIATSGTAK | 1 | Oryza sativa subsp. japonica | T1394 | FATEATSDWLN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T1394 | VATSGTAHFLE | 1 | Arabidopsis thaliana | T1394 | IATSGTAKVLQ | 1 | Oryza sativa subsp. japonica | T1443 | LPNNNTKFVHD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | T1443 | TSSGDALDQKD | 1 | Arabidopsis thaliana | T1443 | TSSGDALDSKD | 1 | Oryza sativa subsp. japonica | T627 | VERSVTGWKEI | 2 | Mus musculus, Rattus norvegicus | T627 | VEKSLLGWKEY | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | T627 | VEKSVTGWKEI | 1 | Homo sapiens | V1170 | VLTKFVEGARE | 2 | Homo sapiens, Mus musculus | V1170 | VLTKFIEGARE | 1 | Rattus norvegicus | V1170 | LVDKYLSDAIE | 1 | Arabidopsis thaliana | V1170 | LVDKYLIDAIE | 1 | Oryza sativa subsp. japonica | V1201 | VEDAGVHSGDA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V1201 | IEQAGVHSGDS | 1 | Arabidopsis thaliana | V1201 | IEQAGIHSGDS | 1 | Oryza sativa subsp. japonica | V626 | LVERSVTGWKE | 2 | Mus musculus, Rattus norvegicus | V626 | LVEKSLLGWKE | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | V626 | LVEKSVTGWKE | 1 | Homo sapiens | V658 | VDAMGVHTGDS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V658 | IDPMGVHTGDS | 2 | Arabidopsis thaliana, Oryza sativa subsp. japonica | W1410 | ATPVAWPSQEG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | W1410 | VERV-LKLHEG | 1 | Arabidopsis thaliana | W1410 | VEPV-LKIHEG | 1 | Oryza sativa subsp. japonica |
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