ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SCN1A

Gene summary

Gene information	Gene symbol	SCN1A
	Gene ID	6323
	Gene name	sodium voltage-gated channel alpha subunit 1
	Synonyms	EIEE6\|FEB3\|FEB3A\|FHM3\|GEFSP2\|HBSCI\|NAC1\|Nav1.1\|SCN1\|SMEI
	Cytomap	2q24.3
	Type of gene	protein-coding
	Description	sodium channel protein type 1 subunit alphasodium channel protein type I subunit alphasodium channel protein, brain I alpha subunitsodium channel voltage gated type 1 alpha subunitsodium channel, voltage-gated, type I, alpha polypeptidesodium channel
	Modification date	20200329
	UniProtAcc	A0A1B0GU68, A0A1B0GUN7, A0A1B0GUX7, A0A1B0GVX7, A0A1B0GWE6, A0A1W2PPJ3, A0A286YEQ8, A0A286YF26, A0A286YFA8, A0A290Y5C0, A0A290Y5I0, A0A2P1H0H1, A0A2P1H0K5, A0A2P1H0L1, A0A2P1H0N9, A0A2P1H0P2, A0A2P1H0R3, A0A2P1H0R4, A0A2P1H0S1, A0A2P1H0S4, A0A2P1H0T0, A0A2P1H0T3, A0A2P1H0T4, A0A2P1H0U7, A0A2R4LFI1, A0A2R4LFM3, A0A2R4LFP2, A0A2R4LFP4, A0A2R4LFR3, A0A2U8RN45, A0A2U8RN66, A0A2U8RN71, A0A2U8RN74, A0A2U8RN75, A0A2U8RN85, A0A5F9ZHI6, F8T7W4, F8T7W5, F8T7W6, F8T7W7, F8T7W8, P35498,
	Context

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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Gene structures and expression levels for SCN1A

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000144285

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
PG	DOWN	ENST00000641575.1	SCN1A-218:protein_coding:SCN1A	2.235618e+02	-8.188065e-01	1.639502e-05	7.263013e-04
PG	DOWN	ENST00000491429.1	SCN1A-205:retained_intron:SCN1A	7.285279e+00	-8.930246e-01	1.064981e-04	2.873546e-03
PG	DOWN	ENST00000651013.1	SCN1A-AS1-214:lncRNA:SCN1A	2.012269e+00	-1.127101e+00	4.263667e-04	7.874753e-03
PG	DOWN	ENST00000409050.1	SCN1A-203:protein_coding:SCN1A	1.877364e+02	-8.191921e-01	2.872914e-03	3.086855e-02
PG	DOWN	ENST00000651782.1	SCN1A-AS1-218:lncRNA:SCN1A	1.197130e+01	-8.160461e-01	3.339723e-03	3.438452e-02
PG	DOWN	ENST00000635750.1	SCN1A-208:protein_coding:SCN1A	1.221434e+02	-1.354596e+00	3.865544e-03	3.817609e-02
CB	UP	ENST00000636759.1	SCN1A-212:nonsense_mediated_decay:SCN1A	6.329321e+00	1.087964e+00	4.177609e-05	3.533811e-04
CB	DOWN	ENST00000660239.1	SCN1A-AS1-221:lncRNA:SCN1A	3.049772e+00	-1.115168e+00	1.254612e-04	8.976823e-04
CB	UP	ENST00000637968.1	SCN1A-215:retained_intron:SCN1A	9.215117e+00	8.858024e-01	3.097920e-04	1.923775e-03
CB	UP	ENST00000507401.2	SCN1A-206:retained_intron:SCN1A	5.427905e+00	1.552112e+00	2.626461e-03	1.155614e-02
CB	DOWN	ENST00000641603.1	SCN1A-219:protein_coding:SCN1A	2.261949e+02	-9.393405e-01	3.813904e-03	1.572458e-02
CB	DOWN	ENST00000447809.2	SCN1A-AS1-201:lncRNA:SCN1A	1.148975e+00	-9.359908e-01	1.309764e-02	4.326232e-02
TC	DOWN	ENST00000409050.1	SCN1A-203:protein_coding:SCN1A	3.992368e+00	-1.295126e+00	2.170518e-03	1.784839e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SCN1A

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_1138	chr2	166077710:166077801:166126924:166127010:166127771:166128015	166126924:166127010
exon_skip_138627	chr2	165998143:165998175:165999051:165999116:165999723:165999776	165999051:165999116
exon_skip_142173	chr2	166039423:166039596:166041231:166041469:166042292:166042424	166041231:166041469
exon_skip_148891	chr2	166037776:166038132:166039423:166039596:166041231:166041469	166039423:166039596
exon_skip_178654	chr2	166058570:166058688:166060640:166060867:166073358:166073565	166060640:166060867
exon_skip_18305	chr2	166073648:166073670:166077710:166077847:166127771:166128015	166077710:166077847
exon_skip_203052	chr2	166073358:166073670:166077710:166077847:166127771:166127866	166077710:166077847
exon_skip_227200	chr2	166002700:166002753:166007230:166007293:166009719:166009841	166007230:166007293
exon_skip_227416	chr2	166039423:166039596:166041215:166041469:166042292:166042424	166041215:166041469
exon_skip_233660	chr2	166077710:166077801:166126924:166127010:166127771:166127866	166126924:166127010
exon_skip_235394	chr2	166073358:166073670:166077710:166077847:166127771:166128015	166077710:166077847
exon_skip_240663	chr2	165999723:165999776:166002472:166002753:166007230:166007293	166002472:166002753
exon_skip_2444	chr2	166046770:166046976:166047627:166047768:166048886:166048949	166047627:166047768
exon_skip_249614	chr2	165999723:165999776:166002472:166002753:166009719:166009841	166002472:166002753
exon_skip_252067	chr2	166002605:166002753:166007230:166007293:166009719:166009841	166007230:166007293
exon_skip_265410	chr2	166073358:166073670:166077710:166077801:166127771:166128015	166077710:166077801
exon_skip_276619	chr2	166015607:166015727:166036048:166036530:166037776:166038132	166036048:166036530
exon_skip_292644	chr2	166058570:166058688:166060640:166060867:166073358:166073670	166060640:166060867
exon_skip_30802	chr2	166058570:166058688:166060640:166060867:166073358:166073621	166060640:166060867
exon_skip_42794	chr2	166051719:166051988:166052852:166052943:166054638:166054766	166052852:166052943
exon_skip_5508	chr2	166073648:166073670:166077710:166077801:166127771:166128015	166077710:166077801
exon_skip_68050	chr2	166073358:166073670:166077710:166077801:166127771:166127866	166077710:166077801
exon_skip_91316	chr2	166002472:166002753:166007230:166007293:166009719:166009841	166007230:166007293

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for SCN1A

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000303395	166077710	166077801	3UTR-3UTR
ENST00000303395	166041231	166041469	Frame-shift
ENST00000303395	166047627	166047768	Frame-shift
ENST00000303395	166002472	166002753	In-frame
ENST00000303395	166036048	166036530	In-frame
ENST00000303395	166039423	166039596	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000303395	166077710	166077801	3UTR-3UTR
ENST00000303395	166002472	166002753	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000303395	166077710	166077801	3UTR-3UTR
ENST00000303395	166047627	166047768	Frame-shift
ENST00000303395	166052852	166052943	Frame-shift
ENST00000303395	166002472	166002753	In-frame
ENST00000303395	166036048	166036530	In-frame

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Infer the effects of exon skipping event on protein functional features for SCN1A

p-ENSG00000144285_img4.png
boxplot

Loci of skipped exons in ROSMAP 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
ENST00000303395	8550	2009	166039423	166039596	2834	3006	805	862
ENST00000303395	8550	2009	166036048	166036530	3365	3846	982	1142
ENST00000303395	8550	2009	166002472	166002753	4421	4701	1334	1427

Loci of skipped exons in MSBB 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
ENST00000303395	8550	2009	166002472	166002753	4421	4701	1334	1427

Loci of skipped exons in Mayo 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
ENST00000303395	8550	2009	166036048	166036530	3365	3846	982	1142
ENST00000303395	8550	2009	166002472	166002753	4421	4701	1334	1427

Lost protein functional features of individual exon skipping events in ROSMAP.

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
P35498	805	862	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	805	862	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	805	862	808	808	Natural variant	ID=VAR_029676;Note=In ICEGTC%3B results in increased peak current density and delayed slow inactivation onset%3B recovery from slow inactivation is delayed. T->S;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12566275,ECO:0000269\|PubMed
P35498	805	862	812	812	Natural variant	ID=VAR_073497;Note=In EIEE6%3B borderline phenotype. T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	805	862	812	812	Natural variant	ID=VAR_064304;Note=In EIEE6. T->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917941,PMID:17054684
P35498	805	862	842	842	Natural variant	ID=VAR_073498;Note=In EIEE6. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	805	862	843	843	Natural variant	ID=VAR_073499;Note=In EIEE6. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	805	862	846	846	Natural variant	ID=VAR_064305;Note=In EIEE6. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917942,PMID:17054684
P35498	805	862	854	855	Natural variant	ID=VAR_073500;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	805	862	859	859	Natural variant	ID=VAR_064306;Note=In GEFS+2 and EIEE6%3B causes a positive shift in the voltage dependence of channel activation%2C slower recovery from slow inactivation and lower levels of current compared with the wild-type channel. R->C;Ontology_term=ECO:0000269,ECO
P35498	805	862	859	859	Natural variant	ID=VAR_073501;Note=In GEFS+2%3B results in impaired channel fast inactivation and significantly increased persistent current. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21864321;Dbxref=dbSNP:rs398123588,PMID:21864321
P35498	805	862	862	862	Natural variant	ID=VAR_064246;Note=In EIEE6. R->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:20110217,ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs121918785,PMID:20110217,PMID:21248271
P35498	805	862	750	1022	Repeat	Note=II;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	805	862	819	832	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	805	862	853	854	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	805	862	799	818	Transmembrane	Note=Helical%3B Name%3DS2 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	805	862	833	852	Transmembrane	Note=Helical%3B Name%3DS3 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	805	862	855	872	Transmembrane	Note=Helical%3B Name%3DS4 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	982	1142	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	982	1142	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	982	1142	982	982	Natural variant	ID=VAR_075569;Note=Found in a patient with acute encephalopathy with biphasic seizures and late reduced diffusion%3B unknown pathological significance. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22309220,ECO:0000269\|PubMed:2631
P35498	982	1142	983	983	Natural variant	ID=VAR_029687;Note=In ICEGTC%3B reduced function%3B decreased peak current density%3B results in a negative shift of inactivation and positive shift of activation. V->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12566275,ECO:0000269
P35498	982	1142	985	985	Natural variant	ID=VAR_029688;Note=In EIEE6. N->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12566275;Dbxref=dbSNP:rs121918747,PMID:12566275
P35498	982	1142	986	986	Natural variant	ID=VAR_014268;Note=In EIEE6%3B complete loss of function. L->F;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11359211,ECO:0000269\|PubMed:14672992;Dbxref=dbSNP:rs121918625,PMID:11359211,PMID:14672992
P35498	982	1142	986	986	Natural variant	ID=VAR_073527;Note=In EIEE6. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	982	1142	987	987	Natural variant	ID=VAR_073528;Note=In EIEE6. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	982	1142	993	993	Natural variant	ID=VAR_073529;Note=In EIEE6%3B borderline phenotype. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	982	1142	998	998	Natural variant	ID=VAR_073530;Note=In EIEE6. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=dbSNP:rs1484321812,PMID:18930999
P35498	982	1142	999	1000	Natural variant	ID=VAR_073531;Note=In EIEE6. NL->LIS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	982	1142	1006	1006	Natural variant	ID=VAR_073532;Note=Probable disease-associated mutation found in a patient with an unclassified form of epilepsy. D->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs375909896,PMID:21248271
P35498	982	1142	1011	1011	Natural variant	ID=VAR_029689;Note=In ICEGTC%3B results in reduced peak current density and hyperpolarizing shift in inactivation. N->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12566275,ECO:0000269\|PubMed:16210358;Dbxref=dbSNP:rs121918759,PMID:12
P35498	982	1142	1034	1034	Natural variant	ID=VAR_029690;Note=Associated with autism. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12610651;Dbxref=dbSNP:rs121918818,PMID:12610651
P35498	982	1142	1038	1038	Natural variant	ID=VAR_029691;Note=Associated with autism. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12610651;Dbxref=PMID:12610651
P35498	982	1142	1067	1067	Natural variant	ID=VAR_014269;Note=A->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11254444,ECO:0000269\|PubMed:12083760,ECO:0000269\|PubMed:12566275,ECO:0000269\|PubMed:12610651,
P35498	982	1142	1068	1068	Natural variant	ID=VAR_073533;Note=In EIEE6. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	982	1142	1079	1079	Natural variant	ID=VAR_073534;Note=V->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:21248271;Dbxref=PMID:18930999,PMID:21248271
P35498	982	1142	1109	1109	Natural variant	ID=VAR_073535;Note=P->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs753452775,PMID:18930999,PMID:21248271
P35498	982	1142	750	1022	Repeat	Note=II;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	982	1142	992	1219	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	982	1142	971	991	Transmembrane	Note=Helical%3B Name%3DS6 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	1334	1427	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	1334	1427	1378	1378	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1392	1392	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1403	1403	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1419	1440	Intramembrane	Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	1334	1427	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	1334	1427	1284	2009	Natural variant	ID=VAR_078727;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1335	1335	Natural variant	ID=VAR_043362;Note=In EIEE6. V->M;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18413471,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917960,PMID:18413471,PMID:20431604
P35498	1334	1427	1339	1339	Natural variant	ID=VAR_073557;Note=In EIEE6. A->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22092154,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs794726789,PMID:22092154,PMID:23195492
P35498	1334	1427	1344	1344	Natural variant	ID=VAR_073558;Note=In EIEE6. I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1345	1345	Natural variant	ID=VAR_078728;Note=In EIEE6. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1350	1350	Natural variant	ID=VAR_073559;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1353	1353	Natural variant	ID=VAR_014272;Note=In GEFS+2%3B complete loss of function. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11254444,ECO:0000269\|PubMed:14672992;Dbxref=dbSNP:rs121917954,PMID:11254444,PMID:14672992
P35498	1334	1427	1355	1355	Natural variant	ID=VAR_029697;Note=In EIEE6. L->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14738421,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs121918776,PMID:14738421,PMID:23195492
P35498	1334	1427	1357	1357	Natural variant	ID=VAR_073560;Note=In ICEGTC. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_073561;Note=In EIEE6. W->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_043363;Note=In EIEE6. W->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18413471;Dbxref=dbSNP:rs121917961,PMID:18413471
P35498	1334	1427	1366	1366	Natural variant	ID=VAR_043364;Note=In GEFS+2 and ICEGTC. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17507202;Dbxref=dbSNP:rs121918805,PMID:17507202
P35498	1334	1427	1367	1367	Natural variant	ID=VAR_064259;Note=In EIEE6. N->K;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:20522430;Dbxref=dbSNP:rs121918760,PMID:18930999,PMID:20522430
P35498	1334	1427	1370	1370	Natural variant	ID=VAR_073562;Note=In EIEE6%3B borderline phenotype. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1376	1376	Natural variant	ID=VAR_073563;Note=In ICEGTC. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073564;Note=In EIEE6. N->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073565;Note=In EIEE6. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs1131691775,PMID:21248271
P35498	1334	1427	1385	1385	Natural variant	ID=VAR_073566;Note=In EIEE6. F->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1390	1390	Natural variant	ID=VAR_029699;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. V->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12083760,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917986,PM
P35498	1334	1427	1391	1391	Natural variant	ID=VAR_073567;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1393	1393	Natural variant	ID=VAR_073568;Note=In EIEE6%3B borderline phenotype. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17129991;Dbxref=PMID:17129991
P35498	1334	1427	1394	1394	Natural variant	ID=VAR_073569;Note=In EIEE6. T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_064260;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16713920,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:19589774;Dbxref=dbSNP:rs121917987,PM
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_073570;Note=In EIEE6. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_073571;Note=In GEFS+2. N->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_064312;Note=In EIEE6. N->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17561957;Dbxref=dbSNP:rs121917925,PMID:17561957
P35498	1334	1427	1416	1416	Natural variant	ID=VAR_073572;Note=In EIEE6. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1417	1417	Natural variant	ID=VAR_073573;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1418	1418	Natural variant	ID=VAR_073574;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1422	1422	Natural variant	ID=VAR_064313;Note=In EIEE6. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917913,PMID:17054684
P35498	1334	1427	1423	1423	Natural variant	ID=VAR_073575;Note=In EIEE6. L->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1426	1426	Natural variant	ID=VAR_064314;Note=In EIEE6. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917944,PMID:17054684
P35498	1334	1427	1427	1427	Natural variant	ID=VAR_073576;Note=In EIEE6. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1200	1514	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1330	1346	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1367	1418	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1347	1366	Transmembrane	Note=Helical%3B Name%3DS5 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

Lost protein functional features of individual exon skipping events in MSBB.

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
P35498	1334	1427	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	1334	1427	1378	1378	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1392	1392	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1403	1403	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1419	1440	Intramembrane	Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	1334	1427	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	1334	1427	1284	2009	Natural variant	ID=VAR_078727;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1335	1335	Natural variant	ID=VAR_043362;Note=In EIEE6. V->M;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18413471,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917960,PMID:18413471,PMID:20431604
P35498	1334	1427	1339	1339	Natural variant	ID=VAR_073557;Note=In EIEE6. A->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22092154,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs794726789,PMID:22092154,PMID:23195492
P35498	1334	1427	1344	1344	Natural variant	ID=VAR_073558;Note=In EIEE6. I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1345	1345	Natural variant	ID=VAR_078728;Note=In EIEE6. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1350	1350	Natural variant	ID=VAR_073559;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1353	1353	Natural variant	ID=VAR_014272;Note=In GEFS+2%3B complete loss of function. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11254444,ECO:0000269\|PubMed:14672992;Dbxref=dbSNP:rs121917954,PMID:11254444,PMID:14672992
P35498	1334	1427	1355	1355	Natural variant	ID=VAR_029697;Note=In EIEE6. L->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14738421,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs121918776,PMID:14738421,PMID:23195492
P35498	1334	1427	1357	1357	Natural variant	ID=VAR_073560;Note=In ICEGTC. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_073561;Note=In EIEE6. W->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_043363;Note=In EIEE6. W->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18413471;Dbxref=dbSNP:rs121917961,PMID:18413471
P35498	1334	1427	1366	1366	Natural variant	ID=VAR_043364;Note=In GEFS+2 and ICEGTC. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17507202;Dbxref=dbSNP:rs121918805,PMID:17507202
P35498	1334	1427	1367	1367	Natural variant	ID=VAR_064259;Note=In EIEE6. N->K;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:20522430;Dbxref=dbSNP:rs121918760,PMID:18930999,PMID:20522430
P35498	1334	1427	1370	1370	Natural variant	ID=VAR_073562;Note=In EIEE6%3B borderline phenotype. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1376	1376	Natural variant	ID=VAR_073563;Note=In ICEGTC. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073564;Note=In EIEE6. N->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073565;Note=In EIEE6. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs1131691775,PMID:21248271
P35498	1334	1427	1385	1385	Natural variant	ID=VAR_073566;Note=In EIEE6. F->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1390	1390	Natural variant	ID=VAR_029699;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. V->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12083760,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917986,PM
P35498	1334	1427	1391	1391	Natural variant	ID=VAR_073567;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1393	1393	Natural variant	ID=VAR_073568;Note=In EIEE6%3B borderline phenotype. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17129991;Dbxref=PMID:17129991
P35498	1334	1427	1394	1394	Natural variant	ID=VAR_073569;Note=In EIEE6. T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_064260;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16713920,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:19589774;Dbxref=dbSNP:rs121917987,PM
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_073570;Note=In EIEE6. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_073571;Note=In GEFS+2. N->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_064312;Note=In EIEE6. N->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17561957;Dbxref=dbSNP:rs121917925,PMID:17561957
P35498	1334	1427	1416	1416	Natural variant	ID=VAR_073572;Note=In EIEE6. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1417	1417	Natural variant	ID=VAR_073573;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1418	1418	Natural variant	ID=VAR_073574;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1422	1422	Natural variant	ID=VAR_064313;Note=In EIEE6. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917913,PMID:17054684
P35498	1334	1427	1423	1423	Natural variant	ID=VAR_073575;Note=In EIEE6. L->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1426	1426	Natural variant	ID=VAR_064314;Note=In EIEE6. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917944,PMID:17054684
P35498	1334	1427	1427	1427	Natural variant	ID=VAR_073576;Note=In EIEE6. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1200	1514	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1330	1346	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1367	1418	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1347	1366	Transmembrane	Note=Helical%3B Name%3DS5 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

Lost protein functional features of individual exon skipping events in Mayo.

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
P35498	982	1142	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	982	1142	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	982	1142	982	982	Natural variant	ID=VAR_075569;Note=Found in a patient with acute encephalopathy with biphasic seizures and late reduced diffusion%3B unknown pathological significance. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22309220,ECO:0000269\|PubMed:2631
P35498	982	1142	983	983	Natural variant	ID=VAR_029687;Note=In ICEGTC%3B reduced function%3B decreased peak current density%3B results in a negative shift of inactivation and positive shift of activation. V->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12566275,ECO:0000269
P35498	982	1142	985	985	Natural variant	ID=VAR_029688;Note=In EIEE6. N->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12566275;Dbxref=dbSNP:rs121918747,PMID:12566275
P35498	982	1142	986	986	Natural variant	ID=VAR_014268;Note=In EIEE6%3B complete loss of function. L->F;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11359211,ECO:0000269\|PubMed:14672992;Dbxref=dbSNP:rs121918625,PMID:11359211,PMID:14672992
P35498	982	1142	986	986	Natural variant	ID=VAR_073527;Note=In EIEE6. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	982	1142	987	987	Natural variant	ID=VAR_073528;Note=In EIEE6. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	982	1142	993	993	Natural variant	ID=VAR_073529;Note=In EIEE6%3B borderline phenotype. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	982	1142	998	998	Natural variant	ID=VAR_073530;Note=In EIEE6. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=dbSNP:rs1484321812,PMID:18930999
P35498	982	1142	999	1000	Natural variant	ID=VAR_073531;Note=In EIEE6. NL->LIS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	982	1142	1006	1006	Natural variant	ID=VAR_073532;Note=Probable disease-associated mutation found in a patient with an unclassified form of epilepsy. D->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs375909896,PMID:21248271
P35498	982	1142	1011	1011	Natural variant	ID=VAR_029689;Note=In ICEGTC%3B results in reduced peak current density and hyperpolarizing shift in inactivation. N->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12566275,ECO:0000269\|PubMed:16210358;Dbxref=dbSNP:rs121918759,PMID:12
P35498	982	1142	1034	1034	Natural variant	ID=VAR_029690;Note=Associated with autism. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12610651;Dbxref=dbSNP:rs121918818,PMID:12610651
P35498	982	1142	1038	1038	Natural variant	ID=VAR_029691;Note=Associated with autism. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12610651;Dbxref=PMID:12610651
P35498	982	1142	1067	1067	Natural variant	ID=VAR_014269;Note=A->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11254444,ECO:0000269\|PubMed:12083760,ECO:0000269\|PubMed:12566275,ECO:0000269\|PubMed:12610651,
P35498	982	1142	1068	1068	Natural variant	ID=VAR_073533;Note=In EIEE6. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	982	1142	1079	1079	Natural variant	ID=VAR_073534;Note=V->I;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:21248271;Dbxref=PMID:18930999,PMID:21248271
P35498	982	1142	1109	1109	Natural variant	ID=VAR_073535;Note=P->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs753452775,PMID:18930999,PMID:21248271
P35498	982	1142	750	1022	Repeat	Note=II;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	982	1142	992	1219	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	982	1142	971	991	Transmembrane	Note=Helical%3B Name%3DS6 of repeat II;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	1334	1427	1	2009	Chain	ID=PRO_0000048489;Note=Sodium channel protein type 1 subunit alpha
P35498	1334	1427	1378	1378	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1392	1392	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1403	1403	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P35498	1334	1427	1419	1440	Intramembrane	Note=Pore-forming;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2
P35498	1334	1427	450	2009	Natural variant	ID=VAR_078726;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25818041;Dbxref=PMID:25818041
P35498	1334	1427	1284	2009	Natural variant	ID=VAR_078727;Note=In EIEE6. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1335	1335	Natural variant	ID=VAR_043362;Note=In EIEE6. V->M;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18413471,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917960,PMID:18413471,PMID:20431604
P35498	1334	1427	1339	1339	Natural variant	ID=VAR_073557;Note=In EIEE6. A->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:22092154,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs794726789,PMID:22092154,PMID:23195492
P35498	1334	1427	1344	1344	Natural variant	ID=VAR_073558;Note=In EIEE6. I->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1345	1345	Natural variant	ID=VAR_078728;Note=In EIEE6. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26993267;Dbxref=PMID:26993267
P35498	1334	1427	1350	1350	Natural variant	ID=VAR_073559;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1353	1353	Natural variant	ID=VAR_014272;Note=In GEFS+2%3B complete loss of function. V->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11254444,ECO:0000269\|PubMed:14672992;Dbxref=dbSNP:rs121917954,PMID:11254444,PMID:14672992
P35498	1334	1427	1355	1355	Natural variant	ID=VAR_029697;Note=In EIEE6. L->P;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14738421,ECO:0000269\|PubMed:23195492;Dbxref=dbSNP:rs121918776,PMID:14738421,PMID:23195492
P35498	1334	1427	1357	1357	Natural variant	ID=VAR_073560;Note=In ICEGTC. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_073561;Note=In EIEE6. W->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1358	1358	Natural variant	ID=VAR_043363;Note=In EIEE6. W->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18413471;Dbxref=dbSNP:rs121917961,PMID:18413471
P35498	1334	1427	1366	1366	Natural variant	ID=VAR_043364;Note=In GEFS+2 and ICEGTC. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17507202;Dbxref=dbSNP:rs121918805,PMID:17507202
P35498	1334	1427	1367	1367	Natural variant	ID=VAR_064259;Note=In EIEE6. N->K;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:18930999,ECO:0000269\|PubMed:20522430;Dbxref=dbSNP:rs121918760,PMID:18930999,PMID:20522430
P35498	1334	1427	1370	1370	Natural variant	ID=VAR_073562;Note=In EIEE6%3B borderline phenotype. A->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1376	1376	Natural variant	ID=VAR_073563;Note=In ICEGTC. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073564;Note=In EIEE6. N->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1378	1378	Natural variant	ID=VAR_073565;Note=In EIEE6. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=dbSNP:rs1131691775,PMID:21248271
P35498	1334	1427	1385	1385	Natural variant	ID=VAR_073566;Note=In EIEE6. F->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1390	1390	Natural variant	ID=VAR_029699;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. V->M;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12083760,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:20431604;Dbxref=dbSNP:rs121917986,PM
P35498	1334	1427	1391	1391	Natural variant	ID=VAR_073567;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1393	1393	Natural variant	ID=VAR_073568;Note=In EIEE6%3B borderline phenotype. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17129991;Dbxref=PMID:17129991
P35498	1334	1427	1394	1394	Natural variant	ID=VAR_073569;Note=In EIEE6. T->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_064260;Note=In EIEE6%3B some patients have a borderline EIEE6 phenotype. C->G;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16713920,ECO:0000269\|PubMed:17347258,ECO:0000269\|PubMed:19589774;Dbxref=dbSNP:rs121917987,PM
P35498	1334	1427	1396	1396	Natural variant	ID=VAR_073570;Note=In EIEE6. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_073571;Note=In GEFS+2. N->D;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1414	1414	Natural variant	ID=VAR_064312;Note=In EIEE6. N->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17561957;Dbxref=dbSNP:rs121917925,PMID:17561957
P35498	1334	1427	1416	1416	Natural variant	ID=VAR_073572;Note=In EIEE6. D->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18930999;Dbxref=PMID:18930999
P35498	1334	1427	1417	1417	Natural variant	ID=VAR_073573;Note=In EIEE6. N->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1418	1418	Natural variant	ID=VAR_073574;Note=In EIEE6. V->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1422	1422	Natural variant	ID=VAR_064313;Note=In EIEE6. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917913,PMID:17054684
P35498	1334	1427	1423	1423	Natural variant	ID=VAR_073575;Note=In EIEE6. L->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248271;Dbxref=PMID:21248271
P35498	1334	1427	1426	1426	Natural variant	ID=VAR_064314;Note=In EIEE6. L->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17054684;Dbxref=dbSNP:rs121917944,PMID:17054684
P35498	1334	1427	1427	1427	Natural variant	ID=VAR_073576;Note=In EIEE6. Q->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23195492;Dbxref=PMID:23195492
P35498	1334	1427	1200	1514	Repeat	Note=III;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1330	1346	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1367	1418	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35498	1334	1427	1347	1366	Transmembrane	Note=Helical%3B Name%3DS5 of repeat III;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:D0E0C2

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3'-UTR located exon skipping events that lost miRNA binding sites in SCN1A

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type	ENST	Exon skip start	Exon skip end	microRNA	Binding site by TargetScan	Binding type by TargetScan	Bdinding site by miRanda	Score of miRanda	Energy by miRanda
Mayo	ENST00000303395	166077710	166077801	hsa-miR-5010-3p	chr2:166077747-166077754	8mer-1a	chr2:166077737-166077758	144.00	-13.09
Mayo	ENST00000303395	166077710	166077801	hsa-miR-4999-5p	chr2:166077771-166077778	8mer-1a	chr2:166077756-166077778	146.00	-16.96
Mayo	ENST00000303395	166077710	166077801	hsa-miR-3138	chr2:166077742-166077749	8mer-1a	chr2:166077733-166077752	154.00	-14.04
Mayo	ENST00000303395	166077710	166077801	hsa-miR-1305	chr2:166077730-166077737	8mer-1a	chr2:166077716-166077737	160.00	-18.29
Mayo	ENST00000303395	166077710	166077801	hsa-miR-147a	chr2:166077745-166077752	8mer-1a	chr2:166077733-166077752	154.00	-14.04
Mayo	ENST00000303395	166077710	166077801	hsa-miR-3911	chr2:166077744-166077751	8mer-1a	chr2:166077733-166077752	154.00	-14.04
MSBB	ENST00000303395	166077710	166077801	hsa-miR-5010-3p	chr2:166077747-166077754	8mer-1a	chr2:166077737-166077758	144.00	-13.09
MSBB	ENST00000303395	166077710	166077801	hsa-miR-4999-5p	chr2:166077771-166077778	8mer-1a	chr2:166077756-166077778	146.00	-16.96
MSBB	ENST00000303395	166077710	166077801	hsa-miR-3138	chr2:166077742-166077749	8mer-1a	chr2:166077733-166077752	154.00	-14.04
MSBB	ENST00000303395	166077710	166077801	hsa-miR-1305	chr2:166077730-166077737	8mer-1a	chr2:166077716-166077737	160.00	-18.29
MSBB	ENST00000303395	166077710	166077801	hsa-miR-147a	chr2:166077745-166077752	8mer-1a	chr2:166077733-166077752	154.00	-14.04
MSBB	ENST00000303395	166077710	166077801	hsa-miR-3911	chr2:166077744-166077751	8mer-1a	chr2:166077733-166077752	154.00	-14.04
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-5010-3p	chr2:166077747-166077754	8mer-1a	chr2:166077737-166077758	144.00	-13.09
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-4999-5p	chr2:166077771-166077778	8mer-1a	chr2:166077756-166077778	146.00	-16.96
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-3138	chr2:166077742-166077749	8mer-1a	chr2:166077733-166077752	154.00	-14.04
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-1305	chr2:166077730-166077737	8mer-1a	chr2:166077716-166077737	160.00	-18.29
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-147a	chr2:166077745-166077752	8mer-1a	chr2:166077733-166077752	154.00	-14.04
ROSMAP	ENST00000303395	166077710	166077801	hsa-miR-3911	chr2:166077744-166077751	8mer-1a	chr2:166077733-166077752	154.00	-14.04

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SNVs in the skipped exons for SCN1A

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for SCN1A

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN1A

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for SCN1A

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	MATR3	exon_skip_227200	-4.388341e-01	4.781688e-07
CB	PCBP1	exon_skip_227200	-4.454432e-01	3.060858e-07
CB	PCBP4	exon_skip_227200	4.129535e-01	2.511753e-06
CB	FUBP1	exon_skip_227200	-4.146219e-01	2.266308e-06
CB	HNRNPA2B1	exon_skip_227200	-4.582309e-01	1.256547e-07
CB	HNRNPF	exon_skip_227200	-4.109433e-01	2.840967e-06
IFG	RBMS3	exon_skip_91316	4.242202e-01	3.455839e-02
IFG	FUBP1	exon_skip_91316	4.219063e-01	3.566283e-02
IFG	TRNAU1AP	exon_skip_1138	5.009948e-01	1.754491e-02
IFG	ESRP1	exon_skip_1138	4.421334e-01	3.936975e-02
PCC	RBM47	exon_skip_1138	-4.130572e-01	1.217564e-08

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RelatedDrugs for SCN1A

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P35498	approved\|vet_approved	DB00252	Phenytoin	small molecule	P35498
P35498	approved	DB00273	Topiramate	small molecule	P35498
P35498	approved\|investigational	DB00313	Valproic Acid	small molecule	P35498
P35498	approved\|investigational	DB00909	Zonisamide	small molecule	P35498
P35498	approved	DB01121	Phenacemide	small molecule	P35498
P35498	approved	DB01438	Phenazopyridine	small molecule	P35498
P35498	approved	DB01595	Nitrazepam	small molecule	P35498
P35498	approved	DB04855	Dronedarone	small molecule	P35498
P35498	approved\|investigational	DB04930	Permethrin	small molecule	P35498
P35498	approved\|investigational	DB05541	Brivaracetam	small molecule	P35498
P35498	approved	DB13269	Dichlorobenzyl alcohol	small molecule	P35498

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RelatedDiseases for SCN1A

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for SCN1A

Gene structures and expression levels for SCN1A

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SCN1A

Open reading frame (ORF) annotation in the exon skipping event for SCN1A

Infer the effects of exon skipping event on protein functional features for SCN1A

3'-UTR located exon skipping events that lost miRNA binding sites in SCN1A

SNVs in the skipped exons for SCN1A

AD stage-associated exon skippint events for SCN1A

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCN1A

Correlation with RNA binding proteins (RBPs) for SCN1A

RelatedDrugs for SCN1A

RelatedDiseases for SCN1A