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 | 1,154 | 129 | 996 |
| Samples | 561 | 76 | 470 |
| Peptides | 420 | 56 | 368 |
Function
SMC1A · Structural maintenance of chromosomes 1A
Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1B or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation. Mutations in this gene result in Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013].
Isoforms & Proteins
3 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.
Gene Properties
Recurrent Mutations
All 411 amino-acid changes on canonical ENST00000322213 · 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 SMC1A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in SMC1A – 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 | 4/40 10% | 0/0 0% |
| Endometrial Carcinoma | 8/42 19% | 48/612 8% |
| Acute Monocytic Leukemia | 0/1 0% | 1/25 4% |
| Acute Myeloid Leukemia | 3/90 3% | 0/0 0% |
| Colorectal Carcinoma | 21/143 15% | 71/3239 2% |
| Cervical Carcinoma | 0/35 0% | 9/422 2% |
| Gastric Carcinoma | 4/74 5% | 32/1809 2% |
| Other Blood Cancers | 1/61 2% | 52/2725 2% |
| Melanoma | 1/210 0% | 37/1899 2% |
| Bladder Carcinoma | 0/58 0% | 18/956 2% |
| Hodgkins Lymphoma | 2/16 12% | 0/122 0% |
| Non-Small Cell Lung Carcinoma | 8/304 3% | 14/1390 1% |
| Ovarian Carcinoma | 2/109 2% | 11/998 1% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 8/810 1% |
| Glioblastoma | 1/98 1% | 0/0 0% |
| Glioma | 0/52 0% | 22/2127 1% |
| Ewings Sarcoma | 1/63 2% | 2/262 1% |
| Head and Neck Carcinoma | 1/85 1% | 14/1574 1% |
| Biliary Tract Carcinoma | 0/54 0% | 9/950 1% |
| Adrenocortical Carcinoma | 0/3 0% | 1/112 1% |
| Neuroendocrine Tumour | 3/154 2% | 3/577 1% |
| Other Solid Cancers | 1/94 1% | 12/1515 1% |
| Small Cell Lung Carcinoma | 0/9 0% | 6/752 1% |
| Other Sarcomas | 2/69 3% | 4/699 1% |
| Breast Carcinoma | 5/144 3% | 21/3264 1% |
| Hepatocellular Carcinoma | 0/46 0% | 16/2210 1% |
| Medulloblastoma | 0/0 0% | 3/450 1% |
| Pancreatic Carcinoma | 1/89 1% | 10/1611 1% |
| Non-Cancerous | 0/104 0% | 6/830 1% |
| Thyroid Gland Carcinoma | 0/45 0% | 10/1592 1% |
Mutation Distribution
Where SMC1A is mutated · all tissues, split by cell line vs tissue
How many mutations in SMC1A 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 1,154 mutations in SMC1A
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 |
|---|