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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 SCN8A |
 Gene summary |
| Gene information | Gene symbol | SCN8A | Gene ID | 6334 |
| Gene name | sodium voltage-gated channel alpha subunit 8 | |
| Synonyms | BFIS5|CERIII|CIAT|EIEE13|MED|NaCh6|Nav1.6|PN4 | |
| Cytomap | 12q13.13 | |
| Type of gene | protein-coding | |
| Description | sodium channel protein type 8 subunit alphahNa6/Scn8a voltage-gated sodium channelsodium channel, voltage gated, type VIII, alpha subunitvoltage-gated sodium channel subunit alpha Nav1.6voltage-gated sodium channel type VIII alpha protein | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UQD0 | |
| Context | PubMed: SCN8A [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 SCN8A 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 SCN8A |
| 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 SCN8A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_82484 | 12 | 52080874:52081003:52082541:52082633:52093353:52093575 | 52082541:52082633 | ENSG00000196876.9 | ENST00000355133.3,ENST00000354534.6,ENST00000545061.1 |
| exon_skip_82485 | 12 | 52080874:52081003:52082788:52082880:52093353:52093575 | 52082788:52082880 | ENSG00000196876.9 | ENST00000550891.1,ENST00000551216.1 |
| exon_skip_82488 | 12 | 52094927:52094991:52096556:52096698:52099200:52099407 | 52096556:52096698 | ENSG00000196876.9 | ENST00000550891.1,ENST00000355133.3,ENST00000551216.1,ENST00000354534.6,ENST00000545061.1 |
| exon_skip_82489 | 12 | 52139686:52139819:52145138:52145377:52156286:52156460 | 52145138:52145377 | ENSG00000196876.9 | ENST00000550891.1,ENST00000355133.3,ENST00000354534.6,ENST00000545061.1 |
| exon_skip_82490 | 12 | 52168023:52168146:52173985:52174055:52180325:52180555 | 52173985:52174055 | ENSG00000196876.9 | ENST00000548086.1 |
| exon_skip_82491 | 12 | 52168023:52168146:52174432:52174555:52180325:52180555 | 52174432:52174555 | ENSG00000196876.9 | ENST00000354534.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SCN8A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_82484 | 12 | 52080874:52081003:52082541:52082633:52093353:52093575 | 52082541:52082633 | ENSG00000196876.9 | ENST00000354534.6,ENST00000545061.1,ENST00000355133.3 |
| exon_skip_82485 | 12 | 52080874:52081003:52082788:52082880:52093353:52093575 | 52082788:52082880 | ENSG00000196876.9 | ENST00000550891.1,ENST00000551216.1 |
| exon_skip_82488 | 12 | 52094927:52094991:52096556:52096698:52099200:52099407 | 52096556:52096698 | ENSG00000196876.9 | ENST00000550891.1,ENST00000354534.6,ENST00000545061.1,ENST00000355133.3,ENST00000551216.1 |
| exon_skip_82489 | 12 | 52139686:52139819:52145138:52145377:52156286:52156460 | 52145138:52145377 | ENSG00000196876.9 | ENST00000550891.1,ENST00000354534.6,ENST00000545061.1,ENST00000355133.3 |
| exon_skip_82490 | 12 | 52168023:52168146:52173985:52174055:52180325:52180555 | 52173985:52174055 | ENSG00000196876.9 | ENST00000548086.1 |
| exon_skip_82491 | 12 | 52168023:52168146:52174432:52174555:52180325:52180555 | 52174432:52174555 | ENSG00000196876.9 | ENST00000354534.6 |
| 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 SCN8A |
| 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 |
| ENST00000354534 | 52082541 | 52082633 | Frame-shift |
| ENST00000354534 | 52096556 | 52096698 | Frame-shift |
| ENST00000354534 | 52145138 | 52145377 | Frame-shift |
| ENST00000354534 | 52174432 | 52174555 | 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 |
| ENST00000354534 | 52082541 | 52082633 | Frame-shift |
| ENST00000354534 | 52096556 | 52096698 | Frame-shift |
| ENST00000354534 | 52145138 | 52145377 | Frame-shift |
| ENST00000354534 | 52174432 | 52174555 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCN8A |
| 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 |
| ENST00000354534 | 11573 | 1980 | 52174432 | 52174555 | 3998 | 4120 | 1273 | 1314 |
| 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 |
| ENST00000354534 | 11573 | 1980 | 52174432 | 52174555 | 3998 | 4120 | 1273 | 1314 |
| 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 |
| Q9UQD0 | 1273 | 1314 | 1275 | 1315 | Alternative sequence | ID=VSP_038651;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19136557;Dbxref=PMID:19136557 |
| Q9UQD0 | 1273 | 1314 | 1275 | 1283 | Alternative sequence | ID=VSP_050592;Note=In isoform 4. SLVSLIANA->PLNLSGLI;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9295353;Dbxref=PMID:9295353 |
| Q9UQD0 | 1273 | 1314 | 1284 | 1980 | Alternative sequence | ID=VSP_050593;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9295353;Dbxref=PMID:9295353 |
| Q9UQD0 | 1273 | 1314 | 1 | 1980 | Chain | ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha |
| Q9UQD0 | 1273 | 1314 | 1279 | 1279 | Natural variant | ID=VAR_078613;Note=In EIEE13. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23708187;Dbxref=PMID:23708187 |
| Q9UQD0 | 1273 | 1314 | 1180 | 1495 | Repeat | Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1283 | 1290 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1310 | 1326 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1264 | 1282 | Transmembrane | Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UQD0 | 1273 | 1314 | 1291 | 1309 | Transmembrane | Note=Helical%3B Name%3DS4 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| 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 |
| Q9UQD0 | 1273 | 1314 | 1275 | 1315 | Alternative sequence | ID=VSP_038651;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:19136557;Dbxref=PMID:19136557 |
| Q9UQD0 | 1273 | 1314 | 1275 | 1283 | Alternative sequence | ID=VSP_050592;Note=In isoform 4. SLVSLIANA->PLNLSGLI;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9295353;Dbxref=PMID:9295353 |
| Q9UQD0 | 1273 | 1314 | 1284 | 1980 | Alternative sequence | ID=VSP_050593;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9295353;Dbxref=PMID:9295353 |
| Q9UQD0 | 1273 | 1314 | 1 | 1980 | Chain | ID=PRO_0000048500;Note=Sodium channel protein type 8 subunit alpha |
| Q9UQD0 | 1273 | 1314 | 1279 | 1279 | Natural variant | ID=VAR_078613;Note=In EIEE13. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23708187;Dbxref=PMID:23708187 |
| Q9UQD0 | 1273 | 1314 | 1180 | 1495 | Repeat | Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1283 | 1290 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1310 | 1326 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UQD0 | 1273 | 1314 | 1264 | 1282 | Transmembrane | Note=Helical%3B Name%3DS3 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UQD0 | 1273 | 1314 | 1291 | 1309 | Transmembrane | Note=Helical%3B Name%3DS4 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
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SNVs in the skipped exons for SCN8A |
| - 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 |
| UVM | TCGA-VD-A8KL-01 | exon_skip_82484 | 52082542 | 52082633 | 52082555 | 52082555 | Frame_Shift_Del | T | - | p.F210fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_82488 | 52096557 | 52096698 | 52096654 | 52096654 | Frame_Shift_Del | T | - | p.F364fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_82489 | 52145139 | 52145377 | 52145227 | 52145227 | Frame_Shift_Del | A | - | p.I740fs |
| KIRP | TCGA-DZ-6133-01 | exon_skip_82489 | 52145139 | 52145377 | 52145329 | 52145329 | Frame_Shift_Del | C | - | p.H774fs |
| KIRP | TCGA-DZ-6133-01 | exon_skip_82489 | 52145139 | 52145377 | 52145329 | 52145329 | Frame_Shift_Del | C | - | p.H775fs |
| PAAD | TCGA-2J-AABV-01 | exon_skip_82489 | 52145139 | 52145377 | 52145205 | 52145205 | Nonsense_Mutation | G | A | p.W733* |
| PAAD | TCGA-2J-AABV-01 | exon_skip_82489 | 52145139 | 52145377 | 52145205 | 52145205 | Nonsense_Mutation | G | A | p.W733X |
| - 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 |
| 451LU_SKIN | 52096557 | 52096698 | 52096584 | 52096584 | Missense_Mutation | G | A | p.M340I |
| MFE319_ENDOMETRIUM | 52096557 | 52096698 | 52096640 | 52096640 | Missense_Mutation | C | T | p.A359V |
| BC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 52145139 | 52145377 | 52145187 | 52145187 | Missense_Mutation | C | T | p.A727V |
| HOP62_LUNG | 52145139 | 52145377 | 52145307 | 52145307 | Missense_Mutation | C | A | p.T767K |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 52174433 | 52174555 | 52174520 | 52174520 | Missense_Mutation | C | T | p.P1303S |
| RKO_LARGE_INTESTINE | 52174433 | 52174555 | 52174544 | 52174544 | Missense_Mutation | G | A | p.E1311K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN8A |
| 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 SCN8A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SCN8A |
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RelatedDrugs for SCN8A |
| 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 |
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RelatedDiseases for SCN8A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SCN8A | C3281191 | EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 13 | 9 | UNIPROT |
| SCN8A | C0005586 | Bipolar Disorder | 2 | PSYGENET |
| SCN8A | C0004134 | Ataxia | 1 | CTD_human |
| SCN8A | C0007758 | Cerebellar Ataxia | 1 | CTD_human;HPO |
| SCN8A | C0014544 | Epilepsy | 1 | CTD_human;HPO |
| SCN8A | C0019372 | Herpesviridae Infections | 1 | CTD_human |
| SCN8A | C0027765 | nervous system disorder | 1 | CTD_human |
| SCN8A | C0032768 | Postherpetic neuralgia | 1 | CTD_human |
| SCN8A | C0038220 | Status Epilepticus | 1 | CTD_human |
| SCN8A | C0040822 | Tremor | 1 | CTD_human |
| SCN8A | C3714756 | Intellectual Disability | 1 | CTD_human;HPO |
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