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 | 11,706 | 1,069 | 10,381 |
| Samples | 1,517 | 225 | 1,272 |
| Peptides | 1,264 | 188 | 1,120 |
Function
SCN5A · Sodium voltage-gated channel alpha subunit 5
The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene have been associated with long QT syndrome type 3 (LQT3), atrial fibrillation, cardiomyopathy, and Brugada syndrome 1, all autosomal dominant cardiac diseases. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2022].
Isoforms & Proteins
8 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 |
|---|---|---|---|
| ENST00000423572 | Q14524-2 | 1,873 | 1,158 |
| ENST00000333535 | Q14524 | 1,715 | 1,109 |
| ENST00000413689 | H9KVD2* | 1,642 | 1,062 |
| ENST00000414099 | E9PG18* | 1,634 | 1,055 |
| ENST00000455624 | E9PHB6* | 1,621 | 1,046 |
| ENST00000449557 | A0A0A0MT39* | 1,616 | 1,039 |
| ENST00000450102 | K4DIA1* | 1,604 | 1,031 |
| ENST00000327956 | Q14524-2 | 1 | 1 |
Gene Properties
Recurrent Mutations
All 1158 amino-acid changes on canonical ENST00000423572 · 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 SCN5A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in SCN5A – 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 | 10/40 25% | 0/0 0% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 18/133 14% |
| Melanoma | 32/210 15% | 252/1899 13% |
| Endometrial Carcinoma | 6/42 14% | 48/612 8% |
| Glioblastoma | 7/98 7% | 0/0 0% |
| Colorectal Carcinoma | 30/143 21% | 182/3239 6% |
| Non-Small Cell Lung Carcinoma | 26/304 9% | 71/1390 5% |
| Gastric Carcinoma | 10/74 14% | 92/1809 5% |
| Other Solid Cancers | 3/94 3% | 77/1515 5% |
| Squamous Cell Lung Carcinoma | 5/57 9% | 38/810 5% |
| Hodgkins Lymphoma | 3/16 19% | 3/122 2% |
| Neuroendocrine Tumour | 15/154 10% | 13/577 2% |
| Bladder Carcinoma | 7/58 12% | 21/956 2% |
| Unknown | 0/10 0% | 1/29 3% |
| Other Sarcomas | 4/69 6% | 15/699 2% |
| Prostate Carcinoma | 3/13 23% | 47/2105 2% |
| Plasma Cell Myeloma | 4/44 9% | 4/305 1% |
| Small Cell Lung Carcinoma | 0/9 0% | 17/752 2% |
| Burkitts Lymphoma | 5/32 16% | 0/196 0% |
| Hepatocellular Carcinoma | 1/46 2% | 47/2210 2% |
| Pancreatic Carcinoma | 2/89 2% | 34/1611 2% |
| Glioma | 2/52 4% | 44/2127 2% |
| Ovarian Carcinoma | 4/109 4% | 19/998 2% |
| Esophageal Carcinoma | 1/23 4% | 15/769 2% |
| Esophageal Squamous Cell Carcinoma | 5/51 10% | 46/2550 2% |
| Head and Neck Carcinoma | 8/85 9% | 23/1574 1% |
| Oral Cavity Carcinoma | 1/54 2% | 0/0 0% |
| Cervical Carcinoma | 0/35 0% | 8/422 2% |
| Breast Carcinoma | 2/144 1% | 50/3264 2% |
| Non-Cancerous | 0/104 0% | 14/830 2% |
Mutation Distribution
Where SCN5A is mutated · all tissues, split by cell line vs tissue
How many mutations in SCN5A 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 54 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 11,706 mutations in SCN5A
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 |
|---|