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 | 1,635 | 206 | 1,396 |
| Samples | 359 | 62 | 287 |
| Peptides | 334 | 49 | 284 |
Function
NPHP1 · Nephrocystin 1
This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Isoforms & Proteins
6 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 270 amino-acid changes on canonical ENST00000393272 · 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 NPHP1 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in NPHP1 – 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 |
|---|---|---|
| Glioblastoma | 4/98 4% | 0/0 0% |
| Endometrial Carcinoma | 5/42 12% | 21/612 3% |
| T-Lymphoblastic Leukemia | 1/40 2% | 0/0 0% |
| Melanoma | 6/210 3% | 41/1899 2% |
| Oral Cavity Carcinoma | 1/54 2% | 0/0 0% |
| Squamous Cell Lung Carcinoma | 3/57 5% | 11/810 1% |
| Hodgkins Lymphoma | 0/16 0% | 2/122 2% |
| Non-Small Cell Lung Carcinoma | 5/304 2% | 19/1390 1% |
| Colorectal Carcinoma | 6/143 4% | 42/3239 1% |
| Cervical Carcinoma | 0/35 0% | 5/422 1% |
| Neuroendocrine Tumour | 5/154 3% | 3/577 1% |
| Ovarian Carcinoma | 5/109 5% | 7/998 1% |
| Hepatocellular Carcinoma | 3/46 7% | 19/2210 1% |
| Other Solid Cancers | 0/94 0% | 15/1515 1% |
| Ewings Sarcoma | 2/63 3% | 1/262 0% |
| Small Cell Lung Carcinoma | 0/9 0% | 7/752 1% |
| Bladder Carcinoma | 0/58 0% | 8/956 1% |
| Gastric Carcinoma | 1/74 1% | 12/1809 1% |
| Esophageal Squamous Cell Carcinoma | 3/51 6% | 15/2550 1% |
| Neuroblastoma | 1/87 1% | 8/1331 1% |
| B-Cell Non-Hodgkins Lymphoma | 3/88 3% | 8/2534 0% |
| Head and Neck Carcinoma | 0/85 0% | 7/1574 0% |
| Glioma | 0/52 0% | 9/2127 0% |
| Other Sarcomas | 0/69 0% | 3/699 0% |
| Meningioma | 1/3 33% | 0/252 0% |
| Breast Carcinoma | 3/144 2% | 10/3264 0% |
| Kidney Carcinoma | 0/85 0% | 7/1862 0% |
| Non-Cancerous | 1/104 1% | 2/830 0% |
| Biliary Tract Carcinoma | 0/54 0% | 3/950 0% |
| Esophageal Carcinoma | 1/23 4% | 1/769 0% |
Mutation Distribution
Where NPHP1 is mutated · all tissues, split by cell line vs tissue
How many mutations in NPHP1 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 1,635 mutations in NPHP1
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 |
|---|