GRCh38 · COSMIC v97
The gene view histogram is a graphical view of mutations across SCN1A. These mutations are displayed at the amino acid level across the full length of the gene by default. Restrict the view to a region of the gene by dragging across the histogram to highlight the region of interest, or by using the sliders in the filters panel to the left. Show more
This default peptide view shows a histogram of single base substitutions, colour coded by residue according to the colour scheme used in Ensembl. Under this is shown the amino acid sequence and the Pfam protein structures, followed by complex mutations and insertions and deletions. The graphical view can be switched to cDNA coordinates by selecting from the "Coordinate system" options in the "Filters" panel on the left.
You can use the filters panel to select the types of data that are
displayed. After adjusting a filter, press
filters, or press
Reset filters to revert to the
original, unfiltered display.
You can see more information on the help pages.
This section gives an overview of SCN1A, along with links to any related data and resources.
Census geneThis is NOT a known cancer gene. It is not found in the Cancer Gene Census.
Curated geneThis is NOT an expert curated gene.Mouse geneMouse insertional mutagenesis experiments DO NOT support the designation of SCN1A as a cancer causing gene.
More informationHallmark geneThis gene does not have a cancer hallmark. You can see more information about hallmarks.
- COSMIC gene
- SCN1A (COSG96024)
- Genomic coordinates
- 2:165989160..166128047 (negative strand)
FEB3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI, CCDS54413.1, P35498
ENSG00000144285.19, NM_001202435.1, NP_001159435,NP_001189364,NP_001340877.1
There is 1 structure for SCN1A. View it in COSMIC-3D.
- Number of samples
42320 unique samples
2461 unique samples with mutations
- Alternative transcripts
- SCN1A_ENST00000640036, SCN1A_ENST00000635750, SCN1A_ENST00000641603, SCN1A_ENST00000423058, SCN1A_ENST00000409050, SCN1A_ENST00000637988, SCN1A_ENST00000635776, SCN1A_ENST00000641575, SCN1A_ENST00000375405
You can see various sequences for this gene:
Protein (SCN1A) Transcript and protein aligned (ENST00000303395.8+SCN1A)
- Gene fusions
- No fusions involving SCN1A
- Drug sensitivity data
This section shows the drugs associated with SCN1A resistance mutations. In the tabs below you can see any other genes that have resistance mutations to the same drug(s), and the distribution of mutations that occur in those genes.
Alternative transcripts are also displayed here for genes where reported resistant mutations are not located on the canonical transcript but are on the alternative, and also where reported resistant mutations are located at the same genomic position on both the canonical and alternative transcripts or on overlapping genes and/or fusions and share a COSM id.
The table shows the distribution of mutations across the primary tissue types that are curated by COSMIC. Histograms show the percentage of mutated samples for point mutations, CNV data and gene expression data. Moving your mouse over the histograms will show additional data. The number of samples tested on this page include samples from the targeted and whole genomes/exome resequencing where all the protein coding genes have been screened for mutations.
You can see additional information about the data presented here in the help pages.
Note that you can also view the genome browser in a separate page.
The genome browser shows COSMIC annotations for SCN1A in a genomic context. Show more
Note: in some web browsers the genome browser may display a blank content panel when switching between browser tabs or when returning to the page using the browser's Back button. If this happens please click and drag the blank content panel to reload the genome browser.
This section displays a series of charts that show the distribution of different types of mutations for SCN1A. Show more
The first chart in this section shows a summary of the types of mutation that have been observed in samples for this gene. The table shows the number of samples recorded as having a particular type of mutation, with the number in brackets giving the percentage of samples with that type of mutation.
Note that a sample may have more than one type of mutation, so the total number of samples determined by simply summing the values in the table may not match the total number of unique samples given under the table. For the same reason, summing the percentages in the table may give a value of greater than 100%.
You can see additional information about this data in the help pages.
This tab displays a table of mutations for the selected gene. You can see more information in our help pages.
This tab displays a table of fusions for the selected gene. You can see more information in our help pages.
|Mutation (Amino Acid)||Mutation ID (COSF)||Count||Mutation Type|
This tab shows a table of gene expression and copy number variation (CNV) data for the selected gene with links to Sample, Study, CNV and (icons) to the ChromoView page (to view CNVs across the whole chromosome), the COSMIC Genome Browser and Ensembl. You can see more information in our help pages.
|Sample||Expression||Expr Level (Z-Score)
Over Expressed; Z-Score > 2.0
Under Expressed; Z-Score < -2.0
Normal; Z-Score within the range -2.0 to 2.0
|CN Type||Minor Allele||Copy Number||CN Segment
1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.
2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.
3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.
This page contains the complete Methylation data for the gene and filter selection(s). Each Methylation probe links to the COSMIC Genome Browser and Ensembl. You can see more information in out help pages.
|Sample Name||Sample ID||Probe ID||Probe Posn.||Type
High (Hypermethylation); Beta-Value > 0.8 and differs from normal average by > 0.5
Low (Hypomethylated); Beta-Value < 0.2 and differs from normal average by > 0.5
|Level (Beta-Value)||Normal Average||Study|
This section shows publications associated with SCN1A. You can see more information in our help pages.
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