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mutLBSgeneDB |
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| Gene summary for GATM |
 Gene summary |
| Basic gene Info. | Gene symbol | GATM |
| Gene name | glycine amidinotransferase (L-arginine:glycine amidinotransferase) | |
| Synonyms | AGAT|AT|CCDS3 | |
| Cytomap | UCSC genome browser: 15q21.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001482.2, | |
| Description | glycine amidinotransferase, mitochondrialtransamidinase | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 602360 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000171766 | ||
| HPRD : 03838 | ||
| Vega : OTTHUMG00000131427 | ||
| Protein | UniProt: P50440 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_GATM | |
| BioGPS: 2628 | ||
| Pathway | NCI Pathway Interaction Database: GATM | |
| KEGG: GATM | ||
| REACTOME: GATM | ||
| Pathway Commons: GATM | ||
| Context | iHOP: GATM | |
| ligand binding site mutation search in PubMed: GATM | ||
| UCL Cancer Institute: GATM | ||
| 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:0006601 | creatine biosynthetic process | 9218780 |
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| Ligand binding site mutations for GATM |
| 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 | G402 | G402E | BLCA | 1 | G402 | G403R | COAD | 1 | N300 | D298G | GBM | 1 | C407 | H406R | KIRC | 1 | N300 | D298Y | 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 GATM |
| 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 | N300 | D298G | -1.032336 | G402 | G402E | -0.68685454 | N300 | D298Y | -0.54006622 | G402 | G403R | -0.39848268 | C407 | H406R | -0.31059057 |
| (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 GATM from PDB |
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| Differential gene expression and gene-gene network for GATM |
| 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 GATM |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C2675179 | Arginine:Glycine Amidinotransferase Deficiency | 3 | Biomarker, GeneticVariation |
| umls:C0018801 | Heart Failure | 1 | Biomarker |
| umls:C0007097 | Carcinoma | 1 | Biomarker |
| umls:C0022658 | Kidney Diseases | 1 | Biomarker |
| umls:C0024667 | Mammary Neoplasms, Animal | 1 | Biomarker |
| umls:C0024668 | Mammary Neoplasms, Experimental | 1 | Biomarker |
| umls:C0151744 | Myocardial Ischemia | 1 | Biomarker |
| umls:C0027540 | Necrosis | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for GATM |
| 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|nutraceutical | DB00129 | L-Ornithine | Small molecule |  |
| Approved|nutraceutical|vet_approved | DB00145 | Glycine | Small molecule |  |
| Experimental | DB02068 | Delta-Amino Valeric Acid | Small molecule |  |
| Experimental | DB02530 | Gamma(Amino)-Butyric Acid | Small molecule |  |
| Experimental | DB04185 | Norvaline | Small molecule |  |
| Experimental | DB04454 | Alpha-Aminobutyric Acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of GATM go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NVA | 2-AMINOPENTANOIC ACID | 1jdx | A | C407 | ARG | ARGININE | 4jdw | A | G402 | ORN | L-ORNITHINE | 3jdw | A | G402 C407 | GLY | GLYCINE RESIDUE | 5jdw | A | N300 G402 C407 | ABU | GAMMA-AMINOBUTYRIC ACID | 6jdw | A | N300 G402 C407 | DAV | DELTA-AMINO VALERIC ACID | 7jdw | A | N300 G402 C407 |
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| Conservation information for LBS of GATM |
| Multiple alignments for P50440 in multiple species |
| LBS | AA sequence | # species | Species | A256 | PCFDAADFIRA | 6 | Homo sapiens, Danio rerio, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | A256 | PCFDAADFMRA | 1 | Xenopus tropicalis | A306 | PMHIDATFNII | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | A306 | PMHIDTTFNII | 1 | Gallus gallus | C407 | GGGFHCWTCDV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | C407 | GGGFHCWTCDI | 2 | Xenopus tropicalis, Gallus gallus | C407 | GGGFHCWTTDV | 1 | Danio rerio | D170 | AAMPRDILLVV | 2 | Xenopus tropicalis, Gallus gallus | D170 | SAMPRDILMVV | 2 | Mus musculus, Rattus norvegicus | D170 | SAMPRDILIVV | 1 | Homo sapiens | D170 | AAMPRDILMVV | 1 | Danio rerio | D170 | GAMPRDILIVV | 1 | Bos taurus | D305 | NPMHIDATFNI | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | D305 | NPMHIDTTFNI | 1 | Gallus gallus | G402 | NANSLGGGFHC | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | G402 | HANSLGGGFHC | 3 | Danio rerio, Xenopus tropicalis, Gallus gallus | H303 | DPNPMHIDATF | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | H303 | DPNPMHIDTTF | 1 | Gallus gallus | L358 | MSSKWLSMNVL | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | M167 | GLYSAMPRDIL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M167 | GMYAAMPRDIL | 3 | Danio rerio, Xenopus tropicalis, Gallus gallus | M167 | GLYGAMPRDIL | 1 | Bos taurus | M302 | KDPNPMHIDAT | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | M302 | KDPNPMHIDTT | 1 | Gallus gallus | N300 | SFKDPNPMHID | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | R169 | YAAMPRDILLV | 2 | Xenopus tropicalis, Gallus gallus | R169 | YSAMPRDILMV | 2 | Mus musculus, Rattus norvegicus | R169 | YSAMPRDILIV | 1 | Homo sapiens | R169 | YAAMPRDILMV | 1 | Danio rerio | R169 | YGAMPRDILIV | 1 | Bos taurus | R322 | LSNPDRPCHQI | 6 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | R322 | LSNPDRPCRQI | 1 | Danio rerio | S354 | HPLWMSSKWLS | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus | S355 | PLWMSSKWLSM | 7 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Bos taurus, Mus musculus, Rattus norvegicus |
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