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 | 616 | 123 | 479 |
| Samples | 188 | 41 | 143 |
| Peptides | 180 | 37 | 147 |
Function
CLN6 · CLN6 transmembrane ER protein
This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008].
Isoforms & Proteins
7 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 |
|---|---|---|---|
| ENST00000249806 | Q9NWW5 | 141 | 106 |
| ENST00000538696 | Q9NWW5-2 | 140 | 97 |
| ENST00000566347 | A0A0S2Z5B7* | 95 | 74 |
| ENST00000564752 | H3BUV4* | 88 | 67 |
| ENST00000637494 | A0A1B0GUD2* | 66 | 57 |
| ENST00000565471 | H3BTY4* | 44 | 37 |
| ENST00000636314 | A0A1B0GUY3* | 42 | 32 |
Gene Properties
Recurrent Mutations
All 97 amino-acid changes on canonical ENST00000538696 · 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 CLN6 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in CLN6 – 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% |
| Thymic Epithelial Tumor | 0/0 0% | 1/39 3% |
| Acute Myeloid Leukemia | 2/90 2% | 0/0 0% |
| Endometrial Carcinoma | 3/42 7% | 5/612 1% |
| Melanoma | 6/210 3% | 19/1899 1% |
| Other Solid Cancers | 0/94 0% | 17/1515 1% |
| Glioblastoma | 1/98 1% | 0/0 0% |
| Esophageal Squamous Cell Carcinoma | 0/51 0% | 26/2550 1% |
| Mesothelioma | 2/62 3% | 0/165 0% |
| Thyroid Gland Carcinoma | 0/45 0% | 9/1592 1% |
| Non-Small Cell Lung Carcinoma | 4/304 1% | 5/1390 0% |
| Gastric Carcinoma | 0/74 0% | 10/1809 1% |
| Germ Cell Tumour | 1/25 4% | 0/169 0% |
| Colorectal Carcinoma | 3/143 2% | 13/3239 0% |
| Ovarian Carcinoma | 2/109 2% | 3/998 0% |
| Neuroendocrine Tumour | 2/154 1% | 1/577 0% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 1/810 0% |
| Biliary Tract Carcinoma | 1/54 2% | 2/950 0% |
| Other Sarcomas | 1/69 1% | 1/699 0% |
| Esophageal Carcinoma | 0/23 0% | 2/769 0% |
| Prostate Carcinoma | 2/13 15% | 3/2105 0% |
| B-Cell Non-Hodgkins Lymphoma | 2/88 2% | 4/2534 0% |
| Glioma | 0/52 0% | 5/2127 0% |
| Cervical Carcinoma | 0/35 0% | 1/422 0% |
| Hepatocellular Carcinoma | 0/46 0% | 5/2210 0% |
| Medulloblastoma | 0/0 0% | 1/450 0% |
| Bladder Carcinoma | 0/58 0% | 2/956 0% |
| Kidney Carcinoma | 0/85 0% | 3/1862 0% |
| Small Cell Lung Carcinoma | 0/9 0% | 1/752 0% |
| Head and Neck Carcinoma | 0/85 0% | 2/1574 0% |
Mutation Distribution
Where CLN6 is mutated · all tissues, split by cell line vs tissue
How many mutations in CLN6 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 616 mutations in CLN6
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 |
|---|