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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for GARS |
 Gene summary |
| Gene information | Gene symbol | GARS | Gene ID | 2617 |
| Gene name | glycyl-tRNA synthetase | |
| Synonyms | CMT2D|DSMAV|GlyRS|HMN5|SMAD1 | |
| Cytomap | 7p14.3 | |
| Type of gene | protein-coding | |
| Description | glycine--tRNA ligaseAP-4-A synthetaseCharcot-Marie-Tooth neuropathy 2DCharcot-Marie-Tooth neuropathy, neuronal type, Ddiadenosine tetraphosphate synthetase | |
| Modification date | 20180523 | |
| UniProtAcc | P41250 | |
| Context | PubMed: GARS [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| GARS | GO:0015966 | diadenosine tetraphosphate biosynthetic process | 19710017 |
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Exon skipping events across known transcript of Ensembl for GARS from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for GARS |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for GARS |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_465137 | 7 | 30634499:30634759:30635439:30635549:30638411:30638513 | 30635439:30635549 | ENSG00000106105.9 | ENST00000454308.1 |
| exon_skip_465138 | 7 | 30634499:30634759:30638411:30638513:30639562:30639665 | 30638411:30638513 | ENSG00000106105.9 | ENST00000478124.1 |
| exon_skip_465140 | 7 | 30649200:30649346:30651711:30651861:30655511:30655674 | 30651711:30651861 | ENSG00000106105.9 | ENST00000389266.3,ENST00000478124.1 |
| exon_skip_465143 | 7 | 30661944:30662078:30665849:30665935:30668175:30668223 | 30665849:30665935 | ENSG00000106105.9 | ENST00000470392.1,ENST00000389266.3 |
| exon_skip_465144 | 7 | 30665849:30665935:30666672:30666806:30668175:30668223 | 30666672:30666806 | ENSG00000106105.9 | ENST00000444666.1 |
| exon_skip_465146 | 7 | 30668175:30668285:30671063:30671157:30671862:30671923 | 30671063:30671157 | ENSG00000106105.9 | ENST00000389266.3,ENST00000444666.1,ENST00000465748.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GARS |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_465137 | 7 | 30634499:30634759:30635439:30635549:30638411:30638513 | 30635439:30635549 | ENSG00000106105.9 | ENST00000454308.1 |
| exon_skip_465138 | 7 | 30634499:30634759:30638411:30638513:30639562:30639665 | 30638411:30638513 | ENSG00000106105.9 | ENST00000478124.1 |
| exon_skip_465140 | 7 | 30649200:30649346:30651711:30651861:30655511:30655674 | 30651711:30651861 | ENSG00000106105.9 | ENST00000389266.3,ENST00000478124.1 |
| exon_skip_465143 | 7 | 30661944:30662078:30665849:30665935:30668175:30668223 | 30665849:30665935 | ENSG00000106105.9 | ENST00000389266.3,ENST00000470392.1 |
| exon_skip_465144 | 7 | 30665849:30665935:30666672:30666806:30668175:30668223 | 30666672:30666806 | ENSG00000106105.9 | ENST00000444666.1 |
| exon_skip_465146 | 7 | 30668175:30668285:30671063:30671157:30671862:30671923 | 30671063:30671157 | ENSG00000106105.9 | ENST00000389266.3,ENST00000444666.1,ENST00000465748.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for GARS |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000389266 | 30665849 | 30665935 | Frame-shift |
| ENST00000389266 | 30671063 | 30671157 | Frame-shift |
| ENST00000389266 | 30651711 | 30651861 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000389266 | 30665849 | 30665935 | Frame-shift |
| ENST00000389266 | 30671063 | 30671157 | Frame-shift |
| ENST00000389266 | 30651711 | 30651861 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GARS |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000389266 | 2651 | 739 | 30651711 | 30651861 | 1123 | 1272 | 294 | 343 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000389266 | 2651 | 739 | 30651711 | 30651861 | 1123 | 1272 | 294 | 343 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P41250 | 294 | 343 | 287 | 296 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 298 | 300 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZXF |
| P41250 | 294 | 343 | 321 | 330 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 299 | 299 | Binding site | Note=Substrate;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 1 | 739 | Chain | ID=PRO_0000072998;Note=Glycine--tRNA ligase |
| P41250 | 294 | 343 | 301 | 305 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 308 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 339 | 341 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 294 | 294 | Natural variant | ID=VAR_018720;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B does not impair transcription or translation or protein stability%3B contrary to the wild-type protein%2C strongly interacts with NRP1. G->R;Ontology_term=ECO:0000269,ECO |
| P41250 | 294 | 343 | 298 | 298 | Natural variant | ID=VAR_073190;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B demonstrates a change in subcellular location pattern%3B does not associate with granules. P->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:20169446 |
| P41250 | 294 | 343 | 310 | 310 | Natural variant | ID=VAR_079827;Note=Probable disease-associated mutation found in a patient with growth retardation%2C microcephaly%2C thinning of the corpus callosum%2C decreased white matter and brain stem involvement%2C as well as large calvaria%2C cerebellar vermis at |
| P41250 | 294 | 343 | 334 | 334 | Natural variant | ID=VAR_073191;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B demonstrates a change in subcellular location pattern%3B does not associate with granules%3B unknown pathological significance. I->F;Ontology_term=ECO:0000269,ECO:0000269 |
| P41250 | 294 | 343 | 331 | 333 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 341 | 346 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 315 | 317 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P41250 | 294 | 343 | 287 | 296 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 298 | 300 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZXF |
| P41250 | 294 | 343 | 321 | 330 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 299 | 299 | Binding site | Note=Substrate;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 1 | 739 | Chain | ID=PRO_0000072998;Note=Glycine--tRNA ligase |
| P41250 | 294 | 343 | 301 | 305 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 308 | 314 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 339 | 341 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
| P41250 | 294 | 343 | 294 | 294 | Natural variant | ID=VAR_018720;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B does not impair transcription or translation or protein stability%3B contrary to the wild-type protein%2C strongly interacts with NRP1. G->R;Ontology_term=ECO:0000269,ECO |
| P41250 | 294 | 343 | 298 | 298 | Natural variant | ID=VAR_073190;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B demonstrates a change in subcellular location pattern%3B does not associate with granules. P->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:20169446 |
| P41250 | 294 | 343 | 310 | 310 | Natural variant | ID=VAR_079827;Note=Probable disease-associated mutation found in a patient with growth retardation%2C microcephaly%2C thinning of the corpus callosum%2C decreased white matter and brain stem involvement%2C as well as large calvaria%2C cerebellar vermis at |
| P41250 | 294 | 343 | 334 | 334 | Natural variant | ID=VAR_073191;Note=In CMT2D%3B shows a large reduction in aminoacylation activity%3B demonstrates a change in subcellular location pattern%3B does not associate with granules%3B unknown pathological significance. I->F;Ontology_term=ECO:0000269,ECO:0000269 |
| P41250 | 294 | 343 | 331 | 333 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 341 | 346 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19710017;Dbxref=PMID:19710017 |
| P41250 | 294 | 343 | 315 | 317 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2ZT5 |
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SNVs in the skipped exons for GARS |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_465140 | 30651712 | 30651861 | 30651736 | 30651736 | Frame_Shift_Del | G | - | p.Q302fs |
| BLCA | TCGA-MV-A51V-01 | exon_skip_465140 | 30651712 | 30651861 | 30651839 | 30651839 | Nonsense_Mutation | C | T | p.R337* |
| UCEC | TCGA-A5-A0GJ-01 | exon_skip_465140 | 30651712 | 30651861 | 30651839 | 30651839 | Nonsense_Mutation | C | T | p.R337* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| HEC151_ENDOMETRIUM | 30638412 | 30638513 | 30638475 | 30638475 | Missense_Mutation | G | A | p.A96T |
| NCIH2081_LUNG | 30651712 | 30651861 | 30651737 | 30651737 | Missense_Mutation | G | A | p.G303R |
| NCIH2106_LUNG | 30651712 | 30651861 | 30651738 | 30651738 | Missense_Mutation | G | T | p.G303V |
| NB7_AUTONOMIC_GANGLIA | 30651712 | 30651861 | 30651806 | 30651806 | Missense_Mutation | A | T | p.I326F |
| KYSE450_OESOPHAGUS | 30651712 | 30651861 | 30651843 | 30651843 | Missense_Mutation | C | G | p.S338C |
| GOS3_CENTRAL_NERVOUS_SYSTEM | 30665850 | 30665935 | 30665896 | 30665896 | Missense_Mutation | G | A | p.D554N |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30665850 | 30665935 | 30665908 | 30665908 | Missense_Mutation | G | A | p.V558M |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 30665850 | 30665935 | 30665932 | 30665932 | Missense_Mutation | T | C | p.Y566H |
| JHESOAD1_OESOPHAGUS | 30671064 | 30671157 | 30671083 | 30671083 | Missense_Mutation | T | C | p.V610A |
| KMRC3_KIDNEY | 30638412 | 30638513 | 30638513 | 30638513 | Splice_Site | G | A | p.K108K |
| NCIH1573_LUNG | 30665850 | 30665935 | 30665851 | 30665851 | Splice_Site | G | A | p.E539K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GARS |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GARS |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GARS |
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RelatedDrugs for GARS |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P41250 | DB00145 | Glycine | Glycine--tRNA ligase | small molecule | approved|nutraceutical|vet_approved |
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RelatedDiseases for GARS |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| GARS | C1833308 | NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE V | 5 | CTD_human;UNIPROT |
| GARS | C1832274 | Charcot-Marie-Tooth disease, Type 2D | 4 | CTD_human;ORPHANET;UNIPROT |
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