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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 SCN11A |
 Gene summary |
| Gene information | Gene symbol | SCN11A | Gene ID | 11280 |
| Gene name | sodium voltage-gated channel alpha subunit 11 | |
| Synonyms | FEPS3|HSAN7|NAV1.9|NaN|PN5|SCN12A|SNS-2 | |
| Cytomap | 3p22.2 | |
| Type of gene | protein-coding | |
| Description | sodium channel protein type 11 subunit alphaperipheral nerve sodium channel 5sensory neuron sodium channel 2sodium channel protein type XI subunit alphasodium channel, voltage-gated, type XI, alpha polypeptidesodium channel, voltage-gated, type XI, a | |
| Modification date | 20180523 | |
| UniProtAcc | Q9UI33 | |
| Context | PubMed: SCN11A [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 SCN11A 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 SCN11A |
| 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 SCN11A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_382470 | 3 | 38936023:38936455:38938335:38938716:38941384:38941564 | 38938335:38938716 | ENSG00000168356.7 | ENST00000450244.1,ENST00000302328.3,ENST00000456224.3,ENST00000444237.2 |
| exon_skip_382471 | 3 | 38949439:38949613:38950487:38950685:38951556:38951698 | 38950487:38950685 | ENSG00000168356.7 | ENST00000450244.1,ENST00000302328.3,ENST00000456224.3,ENST00000444237.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SCN11A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_382470 | 3 | 38936023:38936455:38938335:38938716:38941384:38941564 | 38938335:38938716 | ENSG00000168356.7 | ENST00000302328.3,ENST00000450244.1,ENST00000456224.3,ENST00000444237.2 |
| exon_skip_382471 | 3 | 38949439:38949613:38950487:38950685:38951556:38951698 | 38950487:38950685 | ENSG00000168356.7 | ENST00000302328.3,ENST00000450244.1,ENST00000456224.3,ENST00000444237.2 |
| 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 SCN11A |
| 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 |
| ENST00000302328 | 38938335 | 38938716 | In-frame |
| ENST00000302328 | 38950487 | 38950685 | 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 |
| ENST00000302328 | 38938335 | 38938716 | In-frame |
| ENST00000302328 | 38950487 | 38950685 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCN11A |
| 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 |
| ENST00000302328 | 6517 | 1791 | 38950487 | 38950685 | 1301 | 1498 | 367 | 433 |
| ENST00000302328 | 6517 | 1791 | 38938335 | 38938716 | 2222 | 2602 | 674 | 801 |
| 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 |
| ENST00000302328 | 6517 | 1791 | 38950487 | 38950685 | 1301 | 1498 | 367 | 433 |
| ENST00000302328 | 6517 | 1791 | 38938335 | 38938716 | 2222 | 2602 | 674 | 801 |
| 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 |
| Q9UI33 | 367 | 433 | 1 | 1791 | Chain | ID=PRO_0000048510;Note=Sodium channel protein type 11 subunit alpha |
| Q9UI33 | 367 | 433 | 345 | 369 | Intramembrane | Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 367 | 433 | 381 | 381 | Natural variant | ID=VAR_076682;Note=In FEPS3%3B causes hyperexcitability of dorsal root ganglion neurons%3B depolarizes resting membrane potential%3B enhances spontaneous firing%3B hyperpolarizes channel activation%3B slows deactivation%3B decreases rates of current decay |
| Q9UI33 | 367 | 433 | 419 | 419 | Natural variant | ID=VAR_076683;Note=K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24776970;Dbxref=dbSNP:rs150269814,PMID:24776970 |
| Q9UI33 | 367 | 433 | 115 | 408 | Repeat | Note=I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 370 | 376 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 403 | 572 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 377 | 402 | Transmembrane | Note=Helical%3B Name%3DS6 of repeat I;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 1 | 1791 | Chain | ID=PRO_0000048510;Note=Sodium channel protein type 11 subunit alpha |
| Q9UI33 | 674 | 801 | 776 | 787 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 674 | 801 | 781 | 781 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UI33 | 674 | 801 | 754 | 774 | Intramembrane | Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 674 | 801 | 681 | 681 | Natural variant | ID=VAR_076685;Note=A->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24776970;Dbxref=PMID:24776970 |
| Q9UI33 | 674 | 801 | 699 | 699 | Natural variant | ID=VAR_076686;Note=In FEPS3%3B causes hyperexcitability of dorsal root ganglion neurons%3B hyperpolarizes channel activation%3B slows deactivation%3B depolarizes steady-state fast-inactivation. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25 |
| Q9UI33 | 674 | 801 | 777 | 777 | Natural variant | ID=VAR_030003;Note=M->R;Dbxref=dbSNP:rs4302324 |
| Q9UI33 | 674 | 801 | 559 | 833 | Repeat | Note=II;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 703 | 703 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 703 | 703 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 688 | 702 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 726 | 753 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 775 | 785 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 668 | 687 | Transmembrane | Note=Helical%3B Voltage-sensor%3B Name%3DS4 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 703 | 725 | Transmembrane | Note=Helical%3B Name%3DS5 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 786 | 811 | Transmembrane | Note=Helical%3B Name%3DS6 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| 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 |
| Q9UI33 | 367 | 433 | 1 | 1791 | Chain | ID=PRO_0000048510;Note=Sodium channel protein type 11 subunit alpha |
| Q9UI33 | 367 | 433 | 345 | 369 | Intramembrane | Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 367 | 433 | 381 | 381 | Natural variant | ID=VAR_076682;Note=In FEPS3%3B causes hyperexcitability of dorsal root ganglion neurons%3B depolarizes resting membrane potential%3B enhances spontaneous firing%3B hyperpolarizes channel activation%3B slows deactivation%3B decreases rates of current decay |
| Q9UI33 | 367 | 433 | 419 | 419 | Natural variant | ID=VAR_076683;Note=K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24776970;Dbxref=dbSNP:rs150269814,PMID:24776970 |
| Q9UI33 | 367 | 433 | 115 | 408 | Repeat | Note=I;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 370 | 376 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 403 | 572 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 367 | 433 | 377 | 402 | Transmembrane | Note=Helical%3B Name%3DS6 of repeat I;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 1 | 1791 | Chain | ID=PRO_0000048510;Note=Sodium channel protein type 11 subunit alpha |
| Q9UI33 | 674 | 801 | 776 | 787 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 674 | 801 | 781 | 781 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UI33 | 674 | 801 | 754 | 774 | Intramembrane | Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:D0E0C2 |
| Q9UI33 | 674 | 801 | 681 | 681 | Natural variant | ID=VAR_076685;Note=A->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24776970;Dbxref=PMID:24776970 |
| Q9UI33 | 674 | 801 | 699 | 699 | Natural variant | ID=VAR_076686;Note=In FEPS3%3B causes hyperexcitability of dorsal root ganglion neurons%3B hyperpolarizes channel activation%3B slows deactivation%3B depolarizes steady-state fast-inactivation. G->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25 |
| Q9UI33 | 674 | 801 | 777 | 777 | Natural variant | ID=VAR_030003;Note=M->R;Dbxref=dbSNP:rs4302324 |
| Q9UI33 | 674 | 801 | 559 | 833 | Repeat | Note=II;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 703 | 703 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 703 | 703 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 688 | 702 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 726 | 753 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 775 | 785 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9UI33 | 674 | 801 | 668 | 687 | Transmembrane | Note=Helical%3B Voltage-sensor%3B Name%3DS4 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 703 | 725 | Transmembrane | Note=Helical%3B Name%3DS5 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q9UI33 | 674 | 801 | 786 | 811 | Transmembrane | Note=Helical%3B Name%3DS6 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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SNVs in the skipped exons for SCN11A |
| - 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-A1EG-01 | exon_skip_382470 | 38938336 | 38938716 | 38938482 | 38938482 | Frame_Shift_Del | C | - | p.D753fs |
| STAD | TCGA-CD-A4MG-01 | exon_skip_382470 | 38938336 | 38938716 | 38938481 | 38938482 | Frame_Shift_Ins | - | C | p.D753fs |
| STAD | TCGA-CD-A4MG-01 | exon_skip_382470 | 38938336 | 38938716 | 38938482 | 38938483 | Frame_Shift_Ins | - | C | p.D753fs |
| LUSC | TCGA-66-2787-01 | exon_skip_382470 | 38938336 | 38938716 | 38938418 | 38938418 | Nonsense_Mutation | C | T | p.W774* |
| - 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 |
| MM127_SKIN | 38938336 | 38938716 | 38938346 | 38938346 | Missense_Mutation | C | T | p.G798E |
| HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38938336 | 38938716 | 38938347 | 38938347 | Missense_Mutation | C | T | p.G798R |
| EN_ENDOMETRIUM | 38938336 | 38938716 | 38938356 | 38938356 | Missense_Mutation | T | C | p.T795A |
| HT115_LARGE_INTESTINE | 38938336 | 38938716 | 38938415 | 38938415 | Missense_Mutation | T | G | p.E775A |
| NO10_CENTRAL_NERVOUS_SYSTEM | 38938336 | 38938716 | 38938440 | 38938440 | Missense_Mutation | C | T | p.G767R |
| TE6_OESOPHAGUS | 38938336 | 38938716 | 38938485 | 38938485 | Missense_Mutation | C | T | p.G752R |
| CL40_LARGE_INTESTINE | 38938336 | 38938716 | 38938499 | 38938499 | Missense_Mutation | C | T | p.R747Q |
| SNU407_LARGE_INTESTINE | 38938336 | 38938716 | 38938584 | 38938584 | Missense_Mutation | C | T | p.G719S |
| WM1799_SKIN | 38938336 | 38938716 | 38938608 | 38938608 | Missense_Mutation | C | T | p.V711M |
| ML1_THYROID | 38938336 | 38938716 | 38938647 | 38938647 | Missense_Mutation | C | T | p.V698I |
| SARC9371_BONE | 38938336 | 38938716 | 38938683 | 38938683 | Missense_Mutation | T | C | p.T686A |
| NCIH748_LUNG | 38938336 | 38938716 | 38938698 | 38938698 | Missense_Mutation | C | A | p.A681S |
| L82_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38950488 | 38950685 | 38950495 | 38950495 | Missense_Mutation | T | A | p.E431V |
| TM31_CENTRAL_NERVOUS_SYSTEM | 38950488 | 38950685 | 38950633 | 38950633 | Missense_Mutation | A | G | p.F385S |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 38938336 | 38938716 | 38938347 | 38938347 | Nonsense_Mutation | C | A | p.G798* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN11A |
| 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 SCN11A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SCN11A |
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RelatedDrugs for SCN11A |
| 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 |
| Q9UI33 | DB00907 | Cocaine | Sodium channel protein type 11 subunit alpha | small molecule | approved|illicit | |
| Q9UI33 | DB00909 | Zonisamide | Sodium channel protein type 11 subunit alpha | small molecule | approved|investigational |
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RelatedDiseases for SCN11A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SCN11A | C3809899 | EPISODIC PAIN SYNDROME, FAMILIAL, 3 | 4 | ORPHANET;UNIPROT |
| SCN11A | C3809882 | NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VII | 2 | ORPHANET;UNIPROT |
| SCN11A | C0002768 | Congenital Pain Insensitivity | 1 | CTD_human;ORPHANET |
| SCN11A | C0020429 | Hyperalgesia | 1 | CTD_human |
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