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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 SCN9A |
 Gene summary |
| Gene information | Gene symbol | SCN9A | Gene ID | 6335 |
| Gene name | sodium voltage-gated channel alpha subunit 9 | |
| Synonyms | ETHA|FEB3B|GEFSP7|HSAN2D|NE-NA|NENA|Nav1.7|PN1|SFNP | |
| Cytomap | 2q24.3 | |
| Type of gene | protein-coding | |
| Description | sodium channel protein type 9 subunit alphahNE-Naneuroendocrine sodium channelperipheral sodium channel 1sodium channel protein type IX subunit alphasodium channel, voltage-gated, type IX, alpha polypeptidesodium channel, voltage-gated, type IX, alp | |
| Modification date | 20180523 | |
| UniProtAcc | Q15858 | |
| Context | PubMed: SCN9A [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 |
| SCN9A | GO:0035725 | sodium ion transmembrane transport | 17145499 |
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Exon skipping events across known transcript of Ensembl for SCN9A 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 SCN9A |
| 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 SCN9A |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_344646 | 2 | 167055181:167056374:167060464:167060735:167060869:167060974 | 167060464:167060735 | ENSG00000169432.10 | ENST00000375387.4,ENST00000409435.1,ENST00000303354.6,ENST00000409672.1 |
| exon_skip_344648 | 2 | 167138269:167138318:167140962:167141334:167142845:167143133 | 167140962:167141334 | ENSG00000169432.10 | ENST00000375387.4,ENST00000409435.1,ENST00000452182.1,ENST00000303354.6 |
| exon_skip_344649 | 2 | 167138269:167138318:167140995:167141334:167142845:167143133 | 167140995:167141334 | ENSG00000169432.10 | ENST00000454569.1,ENST00000409672.1 |
| exon_skip_344650 | 2 | 167159599:167159812:167160540:167160632:167162301:167162430 | 167160540:167160632 | ENSG00000169432.10 | ENST00000375387.4,ENST00000454569.1,ENST00000452182.1 |
| exon_skip_344651 | 2 | 167159599:167159812:167160747:167160839:167162301:167162430 | 167160747:167160839 | ENSG00000169432.10 | ENST00000409435.1,ENST00000303354.6,ENST00000409672.1,ENST00000472119.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SCN9A |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_344646 | 2 | 167055181:167056374:167060464:167060735:167060869:167060974 | 167060464:167060735 | ENSG00000169432.10 | ENST00000409672.1,ENST00000375387.4,ENST00000303354.6,ENST00000409435.1 |
| exon_skip_344648 | 2 | 167138269:167138318:167140962:167141334:167142845:167143133 | 167140962:167141334 | ENSG00000169432.10 | ENST00000375387.4,ENST00000303354.6,ENST00000409435.1,ENST00000452182.1 |
| exon_skip_344649 | 2 | 167138269:167138318:167140995:167141334:167142845:167143133 | 167140995:167141334 | ENSG00000169432.10 | ENST00000409672.1,ENST00000454569.1 |
| exon_skip_344650 | 2 | 167159599:167159812:167160540:167160632:167162301:167162430 | 167160540:167160632 | ENSG00000169432.10 | ENST00000375387.4,ENST00000454569.1,ENST00000452182.1 |
| exon_skip_344651 | 2 | 167159599:167159812:167160747:167160839:167162301:167162430 | 167160747:167160839 | ENSG00000169432.10 | ENST00000409672.1,ENST00000303354.6,ENST00000409435.1,ENST00000472119.1 |
| 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 SCN9A |
| 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 |
| ENST00000303354 | 167060464 | 167060735 | Frame-shift |
| ENST00000303354 | 167160747 | 167160839 | Frame-shift |
| ENST00000303354 | 167140962 | 167141334 | 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 |
| ENST00000303354 | 167060464 | 167060735 | Frame-shift |
| ENST00000303354 | 167160747 | 167160839 | Frame-shift |
| ENST00000303354 | 167140962 | 167141334 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCN9A |
| 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 |
| ENST00000303354 | 9804 | 1988 | 167140962 | 167141334 | 1947 | 2318 | 535 | 659 |
| 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 |
| ENST00000303354 | 9804 | 1988 | 167140962 | 167141334 | 1947 | 2318 | 535 | 659 |
| 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 |
| 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 |
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SNVs in the skipped exons for SCN9A |
| - 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 |
| KIRC | TCGA-B0-5099-01 | exon_skip_344646 | 167060465 | 167060735 | 167060645 | 167060645 | Frame_Shift_Del | T | - | p.M1521fs |
| KIRC | TCGA-B0-5099-01 | exon_skip_344646 | 167060465 | 167060735 | 167060645 | 167060645 | Frame_Shift_Del | T | - | p.M1534fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141111 | 167141111 | Frame_Shift_Del | G | - | p.P611fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141111 | 167141111 | Frame_Shift_Del | G | - | p.P611fs |
| BRCA | TCGA-A2-A1FZ-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141168 | 167141171 | Frame_Shift_Del | ACAA | - | p.F589fs |
| BRCA | TCGA-A2-A1FZ-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141168 | 167141171 | Frame_Shift_Del | ACAA | - | p.F589fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.F579fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.G579fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.F579fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.G579fs |
| STAD | TCGA-HU-A4H3-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.F578fs |
| STAD | TCGA-HU-A4H3-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.G579fs |
| STAD | TCGA-HU-A4H3-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.F578fs |
| STAD | TCGA-HU-A4H3-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141203 | 167141203 | Frame_Shift_Del | A | - | p.G579fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141267 | 167141267 | Frame_Shift_Del | A | - | p.F558fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141267 | 167141267 | Frame_Shift_Del | A | - | p.F558fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_344650 | 167160541 | 167160632 | 167160559 | 167160559 | Frame_Shift_Del | T | - | p.T225fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_344651 | 167160748 | 167160839 | 167160766 | 167160766 | Frame_Shift_Del | T | - | p.T225fs |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R597* |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R597X |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140963 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R598* |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R597* |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R597X |
| PAAD | TCGA-IB-A7M4-01 | exon_skip_344648 exon_skip_344649 | 167140996 | 167141334 | 167141148 | 167141148 | Nonsense_Mutation | G | A | p.R598* |
| UCEC | TCGA-AP-A056-01 | exon_skip_344651 | 167160748 | 167160839 | 167160829 | 167160829 | Nonsense_Mutation | C | A | p.E203* |
| UCEC | TCGA-AX-A05Z-01 | exon_skip_344651 | 167160748 | 167160839 | 167160829 | 167160829 | Nonsense_Mutation | C | A | p.E203* |
| UCEC | TCGA-B5-A11E-01 | exon_skip_344651 | 167160748 | 167160839 | 167160829 | 167160829 | Nonsense_Mutation | C | A | p.E203* |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_344650 | 167160541 | 167160632 | 167160633 | 167160633 | Splice_Site | C | A | e5-1 |
| - 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 |
| GP2D_LARGE_INTESTINE | 167140963 | 167141334 | 167141162 | 167141163 | Frame_Shift_Ins | - | G | p.H592fs |
| GP2D_LARGE_INTESTINE | 167140996 | 167141334 | 167141162 | 167141163 | Frame_Shift_Ins | - | G | p.H592fs |
| GP5D_LARGE_INTESTINE | 167140963 | 167141334 | 167141162 | 167141163 | Frame_Shift_Ins | - | G | p.H592fs |
| GP5D_LARGE_INTESTINE | 167140996 | 167141334 | 167141162 | 167141163 | Frame_Shift_Ins | - | G | p.H592fs |
| SKMEL1_SKIN | 167060465 | 167060735 | 167060630 | 167060630 | Missense_Mutation | C | T | p.E1537K |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167060465 | 167060735 | 167060662 | 167060662 | Missense_Mutation | C | T | p.C1526Y |
| JHUEM7_ENDOMETRIUM | 167060465 | 167060735 | 167060696 | 167060696 | Missense_Mutation | G | T | p.Q1515K |
| RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140963 | 167141334 | 167141037 | 167141037 | Missense_Mutation | G | A | p.R634C |
| RPMI6666_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140996 | 167141334 | 167141037 | 167141037 | Missense_Mutation | G | A | p.R634C |
| GIMEN_AUTONOMIC_GANGLIA | 167140963 | 167141334 | 167141091 | 167141091 | Missense_Mutation | C | T | p.G616R |
| GIMEN_AUTONOMIC_GANGLIA | 167140996 | 167141334 | 167141091 | 167141091 | Missense_Mutation | C | T | p.G616R |
| RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140963 | 167141334 | 167141182 | 167141183 | Missense_Mutation | CC | TT | p.R585K |
| RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140996 | 167141334 | 167141182 | 167141183 | Missense_Mutation | CC | TT | p.R585K |
| SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140963 | 167141334 | 167141209 | 167141209 | Missense_Mutation | G | T | p.S576R |
| SUDHL5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167140996 | 167141334 | 167141209 | 167141209 | Missense_Mutation | G | T | p.S576R |
| HEC50B_ENDOMETRIUM | 167140963 | 167141334 | 167141265 | 167141265 | Missense_Mutation | T | G | p.K558Q |
| HEC50B_ENDOMETRIUM | 167140996 | 167141334 | 167141265 | 167141265 | Missense_Mutation | T | G | p.K558Q |
| CAL54_KIDNEY | 167140963 | 167141334 | 167141294 | 167141294 | Missense_Mutation | C | T | p.R548Q |
| CAL54_KIDNEY | 167140996 | 167141334 | 167141294 | 167141294 | Missense_Mutation | C | T | p.R548Q |
| NCIH2172_LUNG | 167140963 | 167141334 | 167141318 | 167141318 | Missense_Mutation | C | A | p.R540L |
| NCIH2172_LUNG | 167140996 | 167141334 | 167141318 | 167141318 | Missense_Mutation | C | A | p.R540L |
| HT55_LARGE_INTESTINE | 167160748 | 167160839 | 167160826 | 167160826 | Missense_Mutation | A | T | p.F204I |
| OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 167160748 | 167160839 | 167160749 | 167160749 | Splice_Site | T | C | p.P229P |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN9A |
| 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 SCN9A |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SCN9A |
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RelatedDrugs for SCN9A |
| 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 |
| Q15858 | DB06201 | Rufinamide | Sodium channel protein type 9 subunit alpha {ECO:0000305} | small molecule | approved | |
| Q15858 | DB06218 | Lacosamide | Sodium channel protein type 9 subunit alpha {ECO:0000305} | small molecule | approved | |
| Q15858 | DB00909 | Zonisamide | Sodium channel protein type 9 subunit alpha {ECO:0000305} | small molecule | approved|investigational | |
| Q15858 | DB00281 | Lidocaine | Sodium channel protein type 9 subunit alpha {ECO:0000305} | small molecule | approved|vet_approved |
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RelatedDiseases for SCN9A |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SCN9A | C0014805 | Primary Erythermalgia | 11 | ORPHANET;UNIPROT |
| SCN9A | C0014804 | Erythromelalgia | 3 | CTD_human;ORPHANET |
| SCN9A | C1833661 | PAROXYSMAL EXTREME PAIN DISORDER | 2 | CTD_human;ORPHANET;UNIPROT |
| SCN9A | C0019372 | Herpesviridae Infections | 1 | CTD_human |
| SCN9A | C0027796 | Neuralgia | 1 | CTD_human |
| SCN9A | C0032768 | Postherpetic neuralgia | 1 | CTD_human |
| SCN9A | C0033774 | Pruritus | 1 | CTD_human;HPO |
| SCN9A | C0150055 | Chronic pain | 1 | CTD_human |
| SCN9A | C1855739 | Indifference to Pain, Congenital, Autosomal Recessive | 1 | CTD_human;UNIPROT |
| SCN9A | C2751778 | Generalized Epilepsy With Febrile Seizures Plus, 7 | 1 | UNIPROT |
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