Stats by Source
Total, split by cell line (COSMIC CL / DepMap / PubMed) vs tissue (COSMIC primary tissue)
Total = all mutations for this gene across every source.
Cell line = COSMIC Cell Lines Project + DepMap + PubMed.
Tissue = COSMIC primary-tissue (patient tumour) samples.
Total can exceed cell line + tissue: COSMIC tissue-derived models sit only in global, and a peptide can be shared across both.
| Total | Cell line | Tissue | |
|---|---|---|---|
| Mutations | 15,909 | 1,525 | 14,178 |
| Samples | 1,502 | 223 | 1,261 |
| Peptides | 1,200 | 178 | 1,062 |
Function
SCN1A · Sodium voltage-gated channel alpha subunit 1
Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015].
Isoforms & Proteins
10 transcripts · UniProt mapping is sequence-verified (AA-safe)
Each Ensembl transcript (ENST) this gene is mutated on, with its matched UniProt accession.
The mapping is sequence-verified: the UniProt sequence is identical to the transcript translation, so amino-acid positions line up exactly. A * marks an unreviewed (TrEMBL) entry.
Counts are mutations and unique mutant peptides on each transcript.
| Transcript | UniProt | Mutations | Peptides |
|---|---|---|---|
| ENST00000674923 | P35498 | 1,759 | 1,132 |
| ENST00000303395 | P35498 | 1,624 | 1,103 |
| ENST00000641575 | A0A286YF26* | 1,622 | 1,101 |
| ENST00000375405 | P35498-2 | 1,621 | 1,100 |
| ENST00000635750 | P35498-2 | 1,621 | 1,100 |
| ENST00000637988 | P35498-2 | 1,621 | 1,100 |
| ENST00000409050 | P35498-3 | 1,611 | 1,091 |
| ENST00000640036 | A0A1W2PPJ3* | 1,594 | 1,084 |
| ENST00000641603 | A0A286YEQ8* | 1,581 | 1,067 |
| ENST00000635776 | A0A1B0GVX7* | 1,255 | 852 |
Gene Properties
Recurrent Mutations
All 1132 amino-acid changes on canonical ENST00000674923 · needle height = samples · drag the mini-map to zoom
A lollipop / needle plot – the standard way to show recurrent mutations along a protein (as used by cBioPortal and MutationMapper).
X-axis = amino-acid position in the protein.
Needle height & head size = how often that exact amino-acid change was observed (its recurrence). Tall/large heads are mutational hotspots.
The most recurrent changes are labelled; hover any needle for the change, position and counts.
Mutation frequency across cancer types
% of samples with a missense/complex mutation in SCN1A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in SCN1A – counted as distinct samples (a sample counts once no matter how many mutations it has).
Split into cell line and tissue; each cell shows mutated / total and the percentage. Cohorts with <20 samples are omitted. Ordered by combined frequency.
| Cancer type | Cell lines | Tissue samples |
|---|---|---|
| T-Lymphoblastic Leukemia | 12/40 30% | 0/0 0% |
| Melanoma | 29/210 14% | 231/1899 12% |
| Endometrial Carcinoma | 8/42 19% | 51/612 8% |
| Squamous Cell Lung Carcinoma | 5/57 9% | 70/810 9% |
| Non-Small Cell Lung Carcinoma | 39/304 13% | 69/1390 5% |
| Other Solid Cancers | 6/94 6% | 93/1515 6% |
| Oral Cavity Carcinoma | 3/54 6% | 0/0 0% |
| Gastric Carcinoma | 3/74 4% | 85/1809 5% |
| Colorectal Carcinoma | 25/143 17% | 132/3239 4% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 6/133 5% |
| Osteosarcoma | 7/45 16% | 1/166 1% |
| Small Cell Lung Carcinoma | 0/9 0% | 28/752 4% |
| Bladder Carcinoma | 2/58 3% | 35/956 4% |
| Neuroendocrine Tumour | 19/154 12% | 7/577 1% |
| Acute Myeloid Leukemia | 3/90 3% | 0/0 0% |
| Esophageal Squamous Cell Carcinoma | 2/51 4% | 77/2550 3% |
| Head and Neck Carcinoma | 3/85 4% | 47/1574 3% |
| Esophageal Carcinoma | 2/23 9% | 20/769 3% |
| Plasma Cell Myeloma | 0/44 0% | 9/305 3% |
| Thymic Epithelial Tumor | 0/0 0% | 1/39 3% |
| Hepatocellular Carcinoma | 0/46 0% | 54/2210 2% |
| Ovarian Carcinoma | 8/109 7% | 15/998 2% |
| Glioblastoma | 2/98 2% | 0/0 0% |
| Non-Cancerous | 1/104 1% | 18/830 2% |
| Other Sarcomas | 6/69 9% | 9/699 1% |
| Biliary Tract Carcinoma | 0/54 0% | 19/950 2% |
| Prostate Carcinoma | 3/13 23% | 32/2105 2% |
| Hodgkins Lymphoma | 1/16 6% | 1/122 1% |
| Pancreatic Carcinoma | 4/89 4% | 20/1611 1% |
| Breast Carcinoma | 4/144 3% | 43/3264 1% |
Mutation Distribution
Where SCN1A is mutated · all tissues, split by cell line vs tissue
How many mutations in SCN1A were found in each tissue, across the whole database.
Each bar is a tissue (cell-line and tissue names are merged to the standard tissue), split into cell line and tissue (patient tumour) contributions.
This shows the cancer-context where this gene is recurrently altered.
GTEx Expression
Median TPM across 52 healthy tissues
Median gene expression (TPM) in normal, non-cancer human tissues from the GTEx project.
Useful for judging tumour specificity – a strong neoantigen target ideally comes from a gene with low expression in healthy tissues.
Scroll or drag the mini-axis below the chart to browse all tissues.
Mutations
All 15,909 mutations in SCN1A
Every mutation record for this gene, across all samples and sources.
The Sample column links to the cell line (cell-line samples) or the tissue type (tissue samples).
Use the Type / Source filters, the search box, and column sorting to explore; each CAN-IMMUNE ID opens the full mutation & peptide view.
| ID | Sample | Transcript | AA Change | CDS | Type | Source | Mutant Peptide | Wild-type Peptide |
|---|