Disease intelligence · mutation landscape
Cutaneous squamous cell carcinoma mutation landscape
How often each gene is altered in cutaneous squamous cell carcinoma, in each sequenced cohort, over the patients on whom it could have been called. Copy number is its own row. Nothing is pooled.
Answer block
In Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021) (83 sequenced patients, exome or genome), the most frequently altered of the 48 genes shown are TP53 66.27%, NOTCH1 55.42%, RELN 46.99%, PKHD1 39.76%, PCDH15 38.55%. Each figure divides by the patients on whom that gene could be called.
Of the briefing's 12 curated targets, 2 are altered in under 2% of this cohort (PDCD1, CD274): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.
2 cohorts are shown and none are pooled; overlap between them has not been checked and there is no disease-wide percentage.
Evidence boundary: frequency here is a count in a named cohort. Whether an alteration is a driver, is actionable, or has a drug is the briefing's question and is not inferred from these numbers.
What is altered, by cohort
One row per alteration, not per gene: a gene that is amplified and rarely mutated (ERBB2, MYCN, EGFR) gets a row for each. Every cell divides by its own denominator — the patients in that cohort on whom that gene could be called. Copy-number rows are shown only where at least one cohort reaches 2%.
| Alteration | cscc_ucsf_2021 83 pts · exome or genome | cscc_hgsc_bcm_2014 39 pts · exome or genome |
|---|---|---|
| TP53 SNV / small indel | 66.27%55/83 | 94.87%37/39 |
| CDKN2A SNV / small indel | 26.51%22/83 | 43.59%17/39 |
| NOTCH1 SNV / small indel | 55.42%46/83 | 58.97%23/39 |
| NOTCH2 SNV / small indel | 36.14%30/83 | 51.28%20/39 |
| EGFR SNV / small indel | 7.23%6/83 | 7.69%3/39 |
| HRAS SNV / small indel | 12.05%10/83 | 20.51%8/39 |
| KMT2D SNV / small indel | 24.1%20/83 | 71.79%28/39 |
| FAT1 SNV / small indel | 30.12%25/83 | 46.15%18/39 |
| PDCD1 SNV / small indel | 1.2%1/83 | 20.51%8/39 |
| CD274 SNV / small indel | 1.2%1/83 | 0% |
| TGFBR1 SNV / small indel | 4.82%4/83 | 7.69%3/39 |
| CASP8 SNV / small indel | 22.89%19/83 | 23.08%9/39 |
| RELN SNV / small indel | 46.99%39/83 | 58.97%23/39 |
| PKHD1 SNV / small indel | 39.76%33/83 | 61.54%24/39 |
| PCDH15 SNV / small indel | 38.55%32/83 | 74.36%29/39 |
| COL6A3 SNV / small indel | 37.35%31/83 | 53.85%21/39 |
| KALRN SNV / small indel | 34.94%29/83 | 38.46%15/39 |
| DCHS2 SNV / small indel | 34.94%29/83 | 51.28%20/39 |
| COL24A1 SNV / small indel | 34.94%29/83 | 46.15%18/39 |
| LAMA2 SNV / small indel | 33.73%28/83 | 46.15%18/39 |
| FSIP2 SNV / small indel | 33.73%28/83 | 28.21%11/39 |
| BLTP1 SNV / small indel | 33.73%28/83 | 43.59%17/39 |
| MDN1 SNV / small indel | 32.53%27/83 | 35.9%14/39 |
| KMT2C SNV / small indel | 32.53%27/83 | 38.46%15/39 |
| ADGRB3 SNV / small indel | 32.53%27/83 | 53.85%21/39 |
| VWF SNV / small indel | 31.33%26/83 | 41.03%16/39 |
| ERICH3 SNV / small indel | 31.33%26/83 | 56.41%22/39 |
| ALMS1 SNV / small indel | 31.33%26/83 | 33.33%13/39 |
| SALL1 SNV / small indel | 30.12%25/83 | 38.46%15/39 |
| ROS1 SNV / small indel | 30.12%25/83 | 48.72%19/39 |
| FMN2 SNV / small indel | 30.12%25/83 | 69.23%27/39 |
| FBN1 SNV / small indel | 30.12%25/83 | 48.72%19/39 |
| PLCE1 SNV / small indel | 28.92%24/83 | 43.59%17/39 |
| DYNC1H1 SNV / small indel | 28.92%24/83 | 38.46%15/39 |
| UNC79 SNV / small indel | 27.71%23/83 | 48.72%19/39 |
| SCN1A SNV / small indel | 27.71%23/83 | 43.59%17/39 |
| PEG3 SNV / small indel | 27.71%23/83 | 46.15%18/39 |
| NF1 SNV / small indel | 27.71%23/83 | 12.82%5/39 |
| MYO16 SNV / small indel | 27.71%23/83 | 51.28%20/39 |
| MYO15A SNV / small indel | 27.71%23/83 | 35.9%14/39 |
| FAM135B SNV / small indel | 27.71%23/83 | 58.97%23/39 |
| COL1A2 SNV / small indel | 27.71%23/83 | 66.67%26/39 |
| ARID2 SNV / small indel | 27.71%23/83 | 17.95%7/39 |
| SLX4 SNV / small indel | 26.51%22/83 | 20.51%8/39 |
| PLCB4 SNV / small indel | 26.51%22/83 | 23.08%9/39 |
| LAMA1 SNV / small indel | 26.51%22/83 | 41.03%16/39 |
| HERC2 SNV / small indel | 26.51%22/83 | 28.21%11/39 |
| FAT2 SNV / small indel | 26.51%22/83 | 48.72%19/39 |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
TP53 is mutated in 55 of 83 patients in Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021).
NOTCH1 is mutated in 46 of 83 patients in Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021).
RELN is mutated in 39 of 83 patients in Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021).
Gene table — reference cohort
Headline values are from the reference cohort, cscc_ucsf_2021; the matrix above keeps every cohort separate. "Curated" marks a gene the disease briefing lists as a target; the rest are here because they are among the most frequently mutated genes in the reference cohort. Recurrent changes are the reference cohort's commonest protein changes.
| Gene | Why listed | Largest alteration | Altered / tested | Frequency | Without hypermutated | Cohorts observed | Range across cohorts | Recurrent changes |
|---|---|---|---|---|---|---|---|---|
| TP53 | curated target | SNV / small indel | 55 / 83 | 66.27% | — | 2 / 2 | 66.27–94.87% | R248Q (n=4), H179Y (n=3), E286K (n=3), G279E (n=2), R196* (n=2) |
| CDKN2A | curated target | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 26.51–43.59% | R7* (n=7), R29* (n=6), P63L (n=3), D33N (n=2), D33G (n=1) |
| NOTCH1 | curated target | SNV / small indel | 46 / 83 | 55.42% | — | 2 / 2 | 55.42–58.97% | R353C (n=3), C423F (n=2), E2071K (n=2), D412Y (n=1), R353G (n=1) |
| NOTCH2 | curated target | SNV / small indel | 30 / 83 | 36.14% | — | 2 / 2 | 36.14–51.28% | G313D (n=2), A1536T (n=1), R452C (n=1), P224L (n=1), W330* (n=1) |
| EGFR | curated target | SNV / small indel | 6 / 83 | 7.23% | — | 2 / 2 | 7.23–7.69% | P150L (n=1), S675F (n=1), V484I (n=1), V416M (n=1), V60M (n=1) |
| HRAS | curated target | SNV / small indel | 10 / 83 | 12.05% | — | 2 / 2 | 12.05–20.51% | Q61L (n=2), G12D (n=2), G13D (n=2), G13R (n=1), Q61K (n=1) |
| KMT2D | curated target | SNV / small indel | 20 / 83 | 24.1% | — | 2 / 2 | 24.1–71.79% | W315* (n=1), A5305V (n=1), G4258S (n=1), P3771L (n=1), D4734N (n=1) |
| FAT1 | curated target | SNV / small indel | 25 / 83 | 30.12% | — | 2 / 2 | 30.12–46.15% | Q3705* (n=2), P4055S (n=1), S4031* (n=1), Q1114* (n=1), R191* (n=1) |
| PDCD1 | curated target | SNV / small indel | 1 / 83 | 1.2% | — | 2 / 2 | 1.2–20.51% | A163V (n=1) |
| CD274 | curated target | SNV / small indel | 1 / 83 | 1.2% | — | 1 / 2 | 0.0–1.2% | none recurrent |
| TGFBR1 | curated target | SNV / small indel | 4 / 83 | 4.82% | — | 2 / 2 | 4.82–7.69% | R80* (n=1), P79S (n=1), V373E (n=1), A310T (n=1) |
| CASP8 | curated target | SNV / small indel | 19 / 83 | 22.89% | — | 2 / 2 | 22.89–23.08% | Q524* (n=2), R494* (n=2), Q398* (n=1), R472* (n=1), Q166* (n=1) |
| RELN | by frequency | SNV / small indel | 39 / 83 | 46.99% | — | 2 / 2 | 46.99–58.97% | W2816* (n=2), A344V (n=2), S825F (n=1), E2298K (n=1), D2479H (n=1) |
| PKHD1 | by frequency | SNV / small indel | 33 / 83 | 39.76% | — | 2 / 2 | 39.76–61.54% | E2148K (n=2), S761T (n=1), P1365L (n=1), W1229* (n=1), P52S (n=1) |
| PCDH15 | by frequency | SNV / small indel | 32 / 83 | 38.55% | — | 2 / 2 | 38.55–74.36% | W1576* (n=2), G1561E (n=1), W1670* (n=1), D333N (n=1), P207S (n=1) |
| COL6A3 | by frequency | SNV / small indel | 31 / 83 | 37.35% | — | 2 / 2 | 37.35–53.85% | P1744S (n=1), F1613S (n=1), G2311R (n=1), P853S (n=1), P347L (n=1) |
| KALRN | by frequency | SNV / small indel | 29 / 83 | 34.94% | — | 2 / 2 | 34.94–38.46% | A630V (n=1), G1435E (n=1), S576L (n=1), S504F (n=1), M1079I (n=1) |
| DCHS2 | by frequency | SNV / small indel | 29 / 83 | 34.94% | — | 2 / 2 | 34.94–51.28% | S1621N (n=1), G2465E (n=1), S549F (n=1), T1574P (n=1), P1644S (n=1) |
| COL24A1 | by frequency | SNV / small indel | 29 / 83 | 34.94% | — | 2 / 2 | 34.94–46.15% | R355C (n=1), G636D (n=1), P1180L (n=1), D1061H (n=1), G1402E (n=1) |
| LAMA2 | by frequency | SNV / small indel | 28 / 83 | 33.73% | — | 2 / 2 | 33.73–46.15% | V2662I (n=1), C390* (n=1), L1733I (n=1), E2335K (n=1), R242C (n=1) |
| FSIP2 | by frequency | SNV / small indel | 28 / 83 | 33.73% | — | 2 / 2 | 28.21–33.73% | K5785E (n=1), Q3316R (n=1), G1610E (n=1), S3939F (n=1), S1564F (n=1) |
| BLTP1 | by frequency | SNV / small indel | 28 / 83 | 33.73% | — | 2 / 2 | 33.73–43.59% | E3514K (n=1), R3177T (n=1), T2557S (n=1), L4865F (n=1), D1975N (n=1) |
| MDN1 | by frequency | SNV / small indel | 27 / 83 | 32.53% | — | 2 / 2 | 32.53–35.9% | F4071L (n=1), S337F (n=1), D3110N (n=1), G1797S (n=1), E5559K (n=1) |
| KMT2C | by frequency | SNV / small indel | 27 / 83 | 32.53% | — | 2 / 2 | 32.53–38.46% | A1685S (n=1), E648K (n=1), S3080* (n=1), S2362L (n=1), L4666V (n=1) |
| ADGRB3 | by frequency | SNV / small indel | 27 / 83 | 32.53% | — | 2 / 2 | 32.53–53.85% | G1020R (n=2), V729A (n=2), P1469L (n=2), A1024V (n=1), G1140S (n=1) |
| VWF | by frequency | SNV / small indel | 26 / 83 | 31.33% | — | 2 / 2 | 31.33–41.03% | P1662A (n=1), P2695L (n=1), S2559L (n=1), V2022M (n=1), M695I (n=1) |
| ERICH3 | by frequency | SNV / small indel | 26 / 83 | 31.33% | — | 2 / 2 | 31.33–56.41% | G479E (n=2), E447K (n=1), G1225E (n=1), E695K (n=1), G1016R (n=1) |
| ALMS1 | by frequency | SNV / small indel | 26 / 83 | 31.33% | — | 2 / 2 | 31.33–33.33% | E2530K (n=1), E3396K (n=1), E2756K (n=1), G706E (n=1), W2427* (n=1) |
| SALL1 | by frequency | SNV / small indel | 25 / 83 | 30.12% | — | 2 / 2 | 30.12–38.46% | P962F (n=1), S20L (n=1), M1247I (n=1), D100N (n=1), H505Y (n=1) |
| ROS1 | by frequency | SNV / small indel | 25 / 83 | 30.12% | — | 2 / 2 | 30.12–48.72% | R466Q (n=1), G2178E (n=1), R1311* (n=1), D869N (n=1), Q412* (n=1) |
| FMN2 | by frequency | SNV / small indel | 25 / 83 | 30.12% | — | 2 / 2 | 30.12–69.23% | E1628K (n=2), P960L (n=1), E1316K (n=1), E750K (n=1), P401L (n=1) |
| FBN1 | by frequency | SNV / small indel | 25 / 83 | 30.12% | — | 2 / 2 | 30.12–48.72% | L1588F (n=1), G2695E (n=1), R2335W (n=1), P1494S (n=1), S1451F (n=1) |
| PLCE1 | by frequency | SNV / small indel | 24 / 83 | 28.92% | — | 2 / 2 | 28.92–43.59% | S1979F (n=2), S1173F (n=2), S205L (n=1), V416A (n=1), R1495Q (n=1) |
| DYNC1H1 | by frequency | SNV / small indel | 24 / 83 | 28.92% | — | 2 / 2 | 28.92–38.46% | H2218Y (n=1), A2258T (n=1), Q3952* (n=1), V2649I (n=1), T240S (n=1) |
| UNC79 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–48.72% | G1835E (n=2), R569Q (n=1), L2278S (n=1), P1385L (n=1), N291T (n=1) |
| SCN1A | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–43.59% | M400I (n=1), H1365Y (n=1), G477D (n=1), E385D (n=1), G1487R (n=1) |
| PEG3 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–46.15% | H527Y (n=1), Q245* (n=1), R963C (n=1), G368E (n=1), S697N (n=1) |
| NF1 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 12.82–27.71% | S2191F (n=1), P866L (n=1), S1759F (n=1), M1539I (n=1), K296K (n=1) |
| MYO16 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–51.28% | G266D (n=2), S91F (n=2), G836K (n=1), P1659S (n=1), P867S (n=1) |
| MYO15A | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–35.9% | M2416I (n=1), S866L (n=1), E518* (n=1), E491D (n=1), E2060K (n=1) |
| FAM135B | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–58.97% | S992F (n=1), P640L (n=1), D1358N (n=1), S540I (n=1), P219L (n=1) |
| COL1A2 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 27.71–66.67% | G445S (n=1), E1134K (n=1), A774D (n=1), G1229E (n=1), P936S (n=1) |
| ARID2 | by frequency | SNV / small indel | 23 / 83 | 27.71% | — | 2 / 2 | 17.95–27.71% | W266* (n=2), F1682Y (n=1), S184* (n=1), Q1403* (n=1), S1435* (n=1) |
| SLX4 | by frequency | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 20.51–26.51% | P170S (n=2), A1286V (n=1), G933D (n=1), R1791C (n=1), L172F (n=1) |
| PLCB4 | by frequency | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 23.08–26.51% | R685* (n=2), E912K (n=1), R51K (n=1), Q793* (n=1), G827E (n=1) |
| LAMA1 | by frequency | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 26.51–41.03% | G614E (n=2), G21A (n=1), G274S (n=1), P2420L (n=1), K2689N (n=1) |
| HERC2 | by frequency | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 26.51–28.21% | A3866V (n=2), P4456L (n=1), A3392D (n=1), S669F (n=1), R3906C (n=1) |
| FAT2 | by frequency | SNV / small indel | 22 / 83 | 26.51% | — | 2 / 2 | 26.51–48.72% | P2068L (n=1), Q1857H (n=1), V855fs (n=1), Q2402* (n=1), R1731* (n=1) |
Cohorts
Listed in the disease profile, not searched: a name search returns the same patients under several accessions. Patients are unique patient ids in the study's sequenced sample list. Hypermutated: more than ten times the cohort's median non-silent mutations per sample, and at least 100.
| Cohort | Accession | Patients | Samples sequenced / in study | Assay | Panels (samples) | Build | Profiles read | Hypermutated patients | Median mutations / sample |
|---|---|---|---|---|---|---|---|---|---|
| Cutaneous Squamous Cell Carcinoma (UCSF, NPJ Genom Med 2021) reference | cscc_ucsf_2021 | 83 observed | 83 / 83 | exome or genome | WES (83) | hg19 | SNV, small indel | 0 | 620 |
| Cutaneous Squamous Cell Carcinoma (MD Anderson, Clin Cancer Res 2014) | cscc_hgsc_bcm_2014 | 39 observed | 39 / 39 | exome or genome | WES (39) | hg19 | SNV, small indel | 0 | 1349 |
Copy-number events
Discrete calls from each study's copy-number profile: 2 is high-level amplification, −2 deep deletion. Gains and shallow losses are not counted. Denominators are the cohort's copy-number sample list, which differs from its sequenced list. Rows at 2% or more.
| Gene | Event | Observed patients | Tested patients | Frequency | Cohort | Profile |
|---|---|---|---|---|---|---|
| No copy-number profile reached 2% for any listed gene, or no cohort carries one. | ||||||
Cohort-aware frequencies
Each row is calculated from unique patients in that study's sequenced sample list. The range is descriptive; no pooled estimate is shown because cross-study overlap and assay comparability have not been checked.
| Gene | Range | Per cohort (altered / tested) |
|---|---|---|
| TP53 | 66.27–94.87% | cscc_ucsf_2021: 55/83 (66.27%) · cscc_hgsc_bcm_2014: 37/39 (94.87%) |
| CDKN2A | 26.51–43.59% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 17/39 (43.59%) |
| NOTCH1 | 55.42–58.97% | cscc_ucsf_2021: 46/83 (55.42%) · cscc_hgsc_bcm_2014: 23/39 (58.97%) |
| NOTCH2 | 36.14–51.28% | cscc_ucsf_2021: 30/83 (36.14%) · cscc_hgsc_bcm_2014: 20/39 (51.28%) |
| EGFR | 7.23–7.69% | cscc_ucsf_2021: 6/83 (7.23%) · cscc_hgsc_bcm_2014: 3/39 (7.69%) |
| HRAS | 12.05–20.51% | cscc_ucsf_2021: 10/83 (12.05%) · cscc_hgsc_bcm_2014: 8/39 (20.51%) |
| KMT2D | 24.1–71.79% | cscc_ucsf_2021: 20/83 (24.1%) · cscc_hgsc_bcm_2014: 28/39 (71.79%) |
| FAT1 | 30.12–46.15% | cscc_ucsf_2021: 25/83 (30.12%) · cscc_hgsc_bcm_2014: 18/39 (46.15%) |
| PDCD1 | 1.2–20.51% | cscc_ucsf_2021: 1/83 (1.2%) · cscc_hgsc_bcm_2014: 8/39 (20.51%) |
| CD274 | 0.0–1.2% | cscc_ucsf_2021: 1/83 (1.2%) · cscc_hgsc_bcm_2014: 0/39 (0.0%) |
| TGFBR1 | 4.82–7.69% | cscc_ucsf_2021: 4/83 (4.82%) · cscc_hgsc_bcm_2014: 3/39 (7.69%) |
| CASP8 | 22.89–23.08% | cscc_ucsf_2021: 19/83 (22.89%) · cscc_hgsc_bcm_2014: 9/39 (23.08%) |
| RELN | 46.99–58.97% | cscc_ucsf_2021: 39/83 (46.99%) · cscc_hgsc_bcm_2014: 23/39 (58.97%) |
| PKHD1 | 39.76–61.54% | cscc_ucsf_2021: 33/83 (39.76%) · cscc_hgsc_bcm_2014: 24/39 (61.54%) |
| PCDH15 | 38.55–74.36% | cscc_ucsf_2021: 32/83 (38.55%) · cscc_hgsc_bcm_2014: 29/39 (74.36%) |
| COL6A3 | 37.35–53.85% | cscc_ucsf_2021: 31/83 (37.35%) · cscc_hgsc_bcm_2014: 21/39 (53.85%) |
| KALRN | 34.94–38.46% | cscc_ucsf_2021: 29/83 (34.94%) · cscc_hgsc_bcm_2014: 15/39 (38.46%) |
| DCHS2 | 34.94–51.28% | cscc_ucsf_2021: 29/83 (34.94%) · cscc_hgsc_bcm_2014: 20/39 (51.28%) |
| COL24A1 | 34.94–46.15% | cscc_ucsf_2021: 29/83 (34.94%) · cscc_hgsc_bcm_2014: 18/39 (46.15%) |
| LAMA2 | 33.73–46.15% | cscc_ucsf_2021: 28/83 (33.73%) · cscc_hgsc_bcm_2014: 18/39 (46.15%) |
| FSIP2 | 28.21–33.73% | cscc_ucsf_2021: 28/83 (33.73%) · cscc_hgsc_bcm_2014: 11/39 (28.21%) |
| BLTP1 | 33.73–43.59% | cscc_ucsf_2021: 28/83 (33.73%) · cscc_hgsc_bcm_2014: 17/39 (43.59%) |
| MDN1 | 32.53–35.9% | cscc_ucsf_2021: 27/83 (32.53%) · cscc_hgsc_bcm_2014: 14/39 (35.9%) |
| KMT2C | 32.53–38.46% | cscc_ucsf_2021: 27/83 (32.53%) · cscc_hgsc_bcm_2014: 15/39 (38.46%) |
| ADGRB3 | 32.53–53.85% | cscc_ucsf_2021: 27/83 (32.53%) · cscc_hgsc_bcm_2014: 21/39 (53.85%) |
| VWF | 31.33–41.03% | cscc_ucsf_2021: 26/83 (31.33%) · cscc_hgsc_bcm_2014: 16/39 (41.03%) |
| ERICH3 | 31.33–56.41% | cscc_ucsf_2021: 26/83 (31.33%) · cscc_hgsc_bcm_2014: 22/39 (56.41%) |
| ALMS1 | 31.33–33.33% | cscc_ucsf_2021: 26/83 (31.33%) · cscc_hgsc_bcm_2014: 13/39 (33.33%) |
| SALL1 | 30.12–38.46% | cscc_ucsf_2021: 25/83 (30.12%) · cscc_hgsc_bcm_2014: 15/39 (38.46%) |
| ROS1 | 30.12–48.72% | cscc_ucsf_2021: 25/83 (30.12%) · cscc_hgsc_bcm_2014: 19/39 (48.72%) |
| FMN2 | 30.12–69.23% | cscc_ucsf_2021: 25/83 (30.12%) · cscc_hgsc_bcm_2014: 27/39 (69.23%) |
| FBN1 | 30.12–48.72% | cscc_ucsf_2021: 25/83 (30.12%) · cscc_hgsc_bcm_2014: 19/39 (48.72%) |
| PLCE1 | 28.92–43.59% | cscc_ucsf_2021: 24/83 (28.92%) · cscc_hgsc_bcm_2014: 17/39 (43.59%) |
| DYNC1H1 | 28.92–38.46% | cscc_ucsf_2021: 24/83 (28.92%) · cscc_hgsc_bcm_2014: 15/39 (38.46%) |
| UNC79 | 27.71–48.72% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 19/39 (48.72%) |
| SCN1A | 27.71–43.59% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 17/39 (43.59%) |
| PEG3 | 27.71–46.15% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 18/39 (46.15%) |
| NF1 | 12.82–27.71% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 5/39 (12.82%) |
| MYO16 | 27.71–51.28% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 20/39 (51.28%) |
| MYO15A | 27.71–35.9% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 14/39 (35.9%) |
| FAM135B | 27.71–58.97% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 23/39 (58.97%) |
| COL1A2 | 27.71–66.67% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 26/39 (66.67%) |
| ARID2 | 17.95–27.71% | cscc_ucsf_2021: 23/83 (27.71%) · cscc_hgsc_bcm_2014: 7/39 (17.95%) |
| SLX4 | 20.51–26.51% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 8/39 (20.51%) |
| PLCB4 | 23.08–26.51% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 9/39 (23.08%) |
| LAMA1 | 26.51–41.03% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 16/39 (41.03%) |
| HERC2 | 26.51–28.21% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 11/39 (28.21%) |
| FAT2 | 26.51–48.72% | cscc_ucsf_2021: 22/83 (26.51%) · cscc_hgsc_bcm_2014: 19/39 (48.72%) |
What this page does not do
Structural variants
Read the structural-variant profiles the studies carry; fusions are the defining event in several of these diseases.
Context
Stage, subtype, age and treatment line are not attached to any count; the cohorts differ on all four.
Interpretation
Activating versus inactivating, actionable versus not, and evidence level are not inferred here; the briefing's target table carries the drug and trial facts.
Limitations
- A cBioPortal public-API snapshot retrieved 2026-09-18; the page does not refresh source data at request time.
- Counts are patients with at least one non-silent call in the study's sequenced sample list; silent, intronic and UTR calls are excluded.
- For targeted-panel cohorts each gene divides by the patients whose panel carried it; a gene absent from the panel is shown as not assayed, not as zero.
- Copy-number rows use discrete calls (2 = high-level amplification, −2 = deep deletion) against the cohort's copy-number sample list, which is a different roster from the sequenced one.
- Cohorts are not pooled. Cross-study patient overlap has not been checked and no disease-wide frequency is reported.
- Structural variants and fusions are not read in this snapshot even where the study carries a profile; germline variants, mutational signatures, TMB and MSI are not reported.
- The gene set is the briefing's curated targets plus the reference cohort's most frequently mutated genes; it is not genome-wide.
How a machine should read this page
- Denominators: every frequency divides by the patients in one named cohort on whom the gene could be called; there is no disease-wide figure.
- Missing values:
not_assayed(the panel did not carry the gene),not_observed(assayed, none found) andnot_evaluable(the cohort could not be read) are three different facts and are never converted to zero. - Counting: patients, not samples; several samples from one patient count once. Non-silent calls only.
- Copy number: a separate assay with a separate roster; discrete calls at ±2 only.
- Hypermutation: flagged per cohort; the headline keeps all patients and the frequency without them is reported beside it.
- Provenance: every value carries the study id, the retrieval date and the processing version; the source is the cBioPortal public API.
Machine endpoints: full landscape · genes · cohorts · the disease's own facts: /disease/cutaneous-squamous-cell-carcinoma.json.
Built by the BioTransfer briefings pipeline from the cBioPortal public API. The neuroblastoma page was assembled by hand and set the rules this page follows; how these are built.