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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 GM2A |
 Gene summary |
| Gene information | Gene symbol | GM2A | Gene ID | 2760 |
| Gene name | GM2 ganglioside activator | |
| Synonyms | GM2-AP|SAP-3 | |
| Cytomap | 5q33.1 | |
| Type of gene | protein-coding | |
| Description | ganglioside GM2 activatorcerebroside sulfate activator proteinshingolipid activator protein 3sphingolipid activator protein 3 | |
| Modification date | 20180519 | |
| UniProtAcc | P17900 | |
| Context | PubMed: GM2A [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 |
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Exon skipping events across known transcript of Ensembl for GM2A 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 GM2A |
| 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 GM2A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_438921 | 5 | 150632452:150632858:150639315:150639477:150646291:150646441 | 150639315:150639477 | ENSG00000196743.4 | ENST00000357164.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GM2A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_438921 | 5 | 150632452:150632858:150639315:150639477:150646291:150646441 | 150639315:150639477 | ENSG00000196743.4 | ENST00000357164.3 |
| 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 GM2A |
| 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 |
| ENST00000357164 | 150639315 | 150639477 | 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 |
| ENST00000357164 | 150639315 | 150639477 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GM2A |
| 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 |
| ENST00000357164 | 3913 | 193 | 150639315 | 150639477 | 407 | 568 | 27 | 81 |
| 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 |
| ENST00000357164 | 3913 | 193 | 150639315 | 150639477 | 407 | 568 | 27 | 81 |
| 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 |
| P17900 | 27 | 81 | 35 | 40 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 45 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 81 | 90 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 32 | 193 | Chain | ID=PRO_0000031640;Note=Ganglioside GM2 activator |
| P17900 | 27 | 81 | 34 | 193 | Chain | ID=PRO_0000031641;Note=Ganglioside GM2 activator isoform short |
| P17900 | 27 | 81 | 39 | 183 | Disulfide bond | . |
| P17900 | 27 | 81 | 63 | 63 | Glycosylation | Note=N-linked (GlcNAc...) asparagine |
| P17900 | 27 | 81 | 59 | 59 | Natural variant | ID=VAR_036892;Note=I->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10364519,ECO:0000269|PubMed:1427911,ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:1915857,ECO:0000269|PubMed:2059210 |
| P17900 | 27 | 81 | 69 | 69 | Natural variant | ID=VAR_036893;Note=M->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10364519,ECO:0000269|PubMed:1427911,ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15489334,ECO:0000269|P |
| P17900 | 27 | 81 | 24 | 31 | Propeptide | ID=PRO_0000031639;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:2209618;Dbxref=PMID:2209618 |
| P17900 | 27 | 81 | 39 | 39 | Sequence conflict | Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P17900 | 27 | 81 | 41 | 43 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| 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 |
| P17900 | 27 | 81 | 35 | 40 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 45 | 74 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 81 | 90 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
| P17900 | 27 | 81 | 32 | 193 | Chain | ID=PRO_0000031640;Note=Ganglioside GM2 activator |
| P17900 | 27 | 81 | 34 | 193 | Chain | ID=PRO_0000031641;Note=Ganglioside GM2 activator isoform short |
| P17900 | 27 | 81 | 39 | 183 | Disulfide bond | . |
| P17900 | 27 | 81 | 63 | 63 | Glycosylation | Note=N-linked (GlcNAc...) asparagine |
| P17900 | 27 | 81 | 59 | 59 | Natural variant | ID=VAR_036892;Note=I->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10364519,ECO:0000269|PubMed:1427911,ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:1915857,ECO:0000269|PubMed:2059210 |
| P17900 | 27 | 81 | 69 | 69 | Natural variant | ID=VAR_036893;Note=M->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10364519,ECO:0000269|PubMed:1427911,ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15489334,ECO:0000269|P |
| P17900 | 27 | 81 | 24 | 31 | Propeptide | ID=PRO_0000031639;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:2209618;Dbxref=PMID:2209618 |
| P17900 | 27 | 81 | 39 | 39 | Sequence conflict | Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P17900 | 27 | 81 | 41 | 43 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AG4 |
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SNVs in the skipped exons for GM2A |
| - 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 |
| SKCM | TCGA-QB-AA9O-06 | exon_skip_438921 | 150639316 | 150639477 | 150639418 | 150639418 | Nonsense_Mutation | G | T | p.G62* |
| - 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 |
| UMUC1_URINARY_TRACT | 150639316 | 150639477 | 150639329 | 150639329 | Missense_Mutation | G | A | p.S32N |
| SW948_LARGE_INTESTINE | 150639316 | 150639477 | 150639356 | 150639356 | Missense_Mutation | A | T | p.E41V |
| HCC2218_BREAST | 150639316 | 150639477 | 150639415 | 150639415 | Missense_Mutation | C | T | p.P61S |
| HCC2218_MATCHED_NORMAL_TISSUE | 150639316 | 150639477 | 150639415 | 150639415 | Missense_Mutation | C | T | p.P61S |
| NCIBL209_MATCHED_NORMAL_TISSUE | 150639316 | 150639477 | 150639415 | 150639415 | Missense_Mutation | C | T | p.P61S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GM2A |
| 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 GM2A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GM2A |
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RelatedDrugs for GM2A |
| 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 |
| P17900 | DB02325 | Isopropyl alcohol | Ganglioside GM2 activator | small molecule | approved|investigational |
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RelatedDiseases for GM2A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| GM2A | C0268275 | Tay-Sachs Disease, AB Variant | 2 | CTD_human;ORPHANET;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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