Disease intelligence · mutation landscape
Melanoma mutation landscape
How often each gene is altered in melanoma, 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 TCGA PanCancer Atlas cutaneous melanoma (2018) (438 sequenced patients, exome or genome), the most frequently altered of the 51 genes shown are BRAF 53.2%, MGAM 39.5%, DSCAM 34.47%, MXRA5 32.65%, PCDH15 32.19%. Each figure divides by the patients on whom that gene could be called.
4 of 438 patients are hypermutated (more than 4390 non-silent mutations, ten times the cohort median of 439); every gene's frequency without them is beside the headline.
Of the briefing's 13 curated targets, 1 are altered in under 2% of this cohort (CTLA4): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.
3 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 | skcm_tcga_pan_can_atlas_2018 438 pts · exome or genome | mel_mskimpact_2020 696 pts · targeted panel | mel_dfci_2019 144 pts · exome or genome |
|---|---|---|---|
| BRAF SNV / small indel | 53.2%233/438 | 43.25%301/696 | 38.89%56/144 |
| BRAF amplification | 4.09%15/367 | 1.72%12/696 | 0.69%1/144 |
| NRAS SNV / small indel | 28.54%125/438 | 29.74%207/696 | 29.86%43/144 |
| NRAS amplification | 3.0%11/367 | 1.44%10/696 | 1.39%2/144 |
| NF1 SNV / small indel | 17.12%75/438 | 27.87%194/696 | 17.36%25/144 |
| KIT SNV / small indel | 6.85%30/438 | 5.6%39/696 | 4.86%7/144 |
| KIT amplification | 2.72%10/367 | 1.29%9/696 | 2.78%4/144 |
| MAP2K1 SNV / small indel | 6.39%28/438 | 8.48%59/696 | 6.94%10/144 |
| CDKN2A SNV / small indel | 13.47%59/438 | 19.97%139/696 | 11.81%17/144 |
| CDKN2A deep deletion | 30.52%112/367 | 25.86%180/696 | 22.22%32/144 |
| PTEN SNV / small indel | 9.82%43/438 | 11.78%82/696 | 7.64%11/144 |
| PTEN deep deletion | 7.63%28/367 | 3.88%27/696 | 5.56%8/144 |
| TERT SNV / small indel | 4.11%18/438 | 9.91%69/696 | 4.17%6/144 |
| TERT amplification | 5.18%19/367 | 2.59%18/696 | 3.47%5/144 |
| PDCD1 SNV / small indel | 3.65%16/438 | 1.87%13/696 | 2.78%4/144 |
| CTLA4 SNV / small indel | 1.37%6/438 | 2.3%16/696 | 2.78%4/144 |
| LAG3 SNV / small indel | 2.74%12/438 | · | 4.86%7/144 |
| MITF SNV / small indel | 2.05%9/438 | 2.16%15/696 | 0.69%1/144 |
| MITF amplification | 6.54%24/367 | 3.45%24/696 | 0.69%1/144 |
| PMEL SNV / small indel | 3.88%17/438 | · | 0.69%1/144 |
| MGAM SNV / small indel | 39.5%173/438 | · | 31.25%45/144 |
| MGAM amplification | 3.27%12/367 | 0% | 0.69%1/144 |
| DSCAM SNV / small indel | 34.47%151/438 | · | 25.0%36/144 |
| MXRA5 SNV / small indel | 32.65%143/438 | · | 33.33%48/144 |
| PCDH15 SNV / small indel | 32.19%141/438 | · | 22.22%32/144 |
| COL4A4 SNV / small indel | 30.82%135/438 | · | 19.44%28/144 |
| SCN11A SNV / small indel | 29.91%131/438 | · | 14.58%21/144 |
| MROH2B SNV / small indel | 29.68%130/438 | · | 19.44%28/144 |
| UNC13C SNV / small indel | 29.0%127/438 | · | 20.14%29/144 |
| SPHKAP SNV / small indel | 29.0%127/438 | · | 22.92%33/144 |
| PTPRT SNV / small indel | 28.31%124/438 | 36.49%254/696 | 24.31%35/144 |
| SCN10A SNV / small indel | 27.63%121/438 | · | 23.61%34/144 |
| FAM135B SNV / small indel | 27.63%121/438 | · | 17.36%25/144 |
| FAM135B amplification | 4.36%16/367 | 0% | 4.17%6/144 |
| ASXL3 SNV / small indel | 27.63%121/438 | · | 22.92%33/144 |
| SVEP1 SNV / small indel | 27.17%119/438 | · | 16.67%24/144 |
| ADGRG4 SNV / small indel | 27.17%119/438 | · | 18.06%26/144 |
| MYH2 SNV / small indel | 26.94%118/438 | · | 23.61%34/144 |
| GRIN2A SNV / small indel | 26.94%118/438 | 31.18%217/696 | 17.36%25/144 |
| RELN SNV / small indel | 26.71%117/438 | · | 20.14%29/144 |
| ERICH3 SNV / small indel | 26.71%117/438 | · | 20.14%29/144 |
| DCC SNV / small indel | 26.03%114/438 | · | 22.92%33/144 |
| SI SNV / small indel | 25.8%113/438 | · | 18.75%27/144 |
| MYH1 SNV / small indel | 25.57%112/438 | · | 18.06%26/144 |
| TACC2 SNV / small indel | 25.11%110/438 | · | 20.14%29/144 |
| STXBP5L SNV / small indel | 24.89%109/438 | · | 13.89%20/144 |
| CACNA1E SNV / small indel | 24.89%109/438 | · | 24.31%35/144 |
| STAB2 SNV / small indel | 24.66%108/438 | · | 22.92%33/144 |
| TRANK1 SNV / small indel | 24.43%107/438 | · | 23.61%34/144 |
| SCN5A SNV / small indel | 24.43%107/438 | · | 13.89%20/144 |
| NPAP1 SNV / small indel | 24.43%107/438 | · | 19.44%28/144 |
| FCGBP SNV / small indel | 24.2%106/438 | · | 18.75%27/144 |
| FCGBP amplification | 0% | 0% | 3.47%5/144 |
| FRAS1 SNV / small indel | 23.97%105/438 | · | 16.67%24/144 |
| C6 SNV / small indel | 23.97%105/438 | · | 18.06%26/144 |
| ADAMTS20 SNV / small indel | 23.97%105/438 | · | 22.22%32/144 |
| COL7A1 SNV / small indel | 23.74%104/438 | · | 16.67%24/144 |
| COL3A1 SNV / small indel | 23.74%104/438 | · | 19.44%28/144 |
| CMYA5 SNV / small indel | 23.74%104/438 | · | 21.53%31/144 |
| CD163 SNV / small indel | 23.74%104/438 | · | 21.53%31/144 |
| TLL1 SNV / small indel | 23.52%103/438 | · | 15.28%22/144 |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
BRAF is mutated in 233 of 438 patients in TCGA PanCancer Atlas cutaneous melanoma (2018).
MGAM is mutated in 173 of 438 patients in TCGA PanCancer Atlas cutaneous melanoma (2018).
DSCAM is mutated in 151 of 438 patients in TCGA PanCancer Atlas cutaneous melanoma (2018).
Gene table — reference cohort
Headline values are from the reference cohort, skcm_tcga_pan_can_atlas_2018; 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 |
|---|---|---|---|---|---|---|---|---|
| BRAF | curated target | SNV / small indel | 233 / 438 | 53.2% | 53.0% | 3 / 3 | 38.89–53.2% | V600E (n=158), V600K (n=35), K601E (n=5), V600R (n=4), G466E (n=4) |
| NRAS | curated target | SNV / small indel | 125 / 438 | 28.54% | 28.8% | 3 / 3 | 28.54–29.86% | Q61R (n=54), Q61K (n=38), Q61L (n=16), Q61H (n=6), G12R (n=2) |
| NF1 | curated target | SNV / small indel | 75 / 438 | 17.12% | 16.36% | 3 / 3 | 17.12–27.87% | R440* (n=5), S2496F (n=2), Q282* (n=2), X69_splice (n=2), Q1070* (n=2) |
| KIT | curated target | SNV / small indel | 30 / 438 | 6.85% | 6.45% | 3 / 3 | 4.86–6.85% | K642E (n=6), V559A (n=3), L576P (n=2), M722I (n=1), W582L (n=1) |
| MAP2K1 | curated target | SNV / small indel | 28 / 438 | 6.39% | 6.45% | 3 / 3 | 6.39–8.48% | P124S (n=13), P124L (n=4), E203K (n=2), K57N (n=2), Q278H (n=1) |
| CDKN2A | curated target | deep deletion | 112 / 367 | 30.52% mutation 13.47% | 13.13% | 3 / 3 | 11.81–19.97% | P114L (n=10), R58* (n=6), W110* (n=5), X51_splice (n=5), Q50* (n=5) |
| PTEN | curated target | SNV / small indel | 43 / 438 | 9.82% | 9.91% | 3 / 3 | 7.64–11.78% | P38S (n=3), V166Sfs*14 (n=3), Q298* (n=2), X342_splice (n=2), R130* (n=1) |
| TERT | curated target | amplification | 19 / 367 | 5.18% mutation 4.11% | 3.69% | 3 / 3 | 4.11–9.91% | G830W (n=1), S802N (n=1), S1095P (n=1), R1105L (n=1), D628N (n=1) |
| PDCD1 | curated target | SNV / small indel | 16 / 438 | 3.65% | 3.69% | 3 / 3 | 1.87–3.65% | H107N (n=2), E211K (n=2), Q88* (n=1), S38F (n=1), S220F (n=1) |
| CTLA4 | curated target | SNV / small indel | 6 / 438 | 1.37% | 1.38% | 3 / 3 | 1.37–2.78% | *224Lext*16 (n=1), Q117* (n=1), G199R (n=1), P137Q (n=1), M91I (n=1) |
| LAG3 | curated target | SNV / small indel | 12 / 438 | 2.74% | 2.53% | 2 / 3 | 2.74–4.86% | G261C (n=1), W16L (n=1), S460F (n=1), I253S (n=1), G365E (n=1) |
| MITF | curated target | amplification | 24 / 367 | 6.54% mutation 2.05% | 2.07% | 3 / 3 | 0.69–2.16% | L106R (n=1), R298S (n=1), L484F (n=1), T127del (n=1), P210Q (n=1) |
| PMEL | curated target | SNV / small indel | 17 / 438 | 3.88% | 3.92% | 2 / 3 | 0.69–3.88% | P214S (n=1), Q583K (n=1), P91T (n=1), E437* (n=1), G228W (n=1) |
| MGAM | by frequency | SNV / small indel | 173 / 438 | 39.5% | 38.94% | 2 / 3 | 31.25–39.5% | P1091L (n=5), R98Q (n=5), R1097C (n=5), E805K (n=3), E435K (n=3) |
| DSCAM | by frequency | SNV / small indel | 151 / 438 | 34.47% | 33.87% | 2 / 3 | 25.0–34.47% | E368K (n=6), E1819K (n=6), D771N (n=5), E1464K (n=5), E1584K (n=4) |
| MXRA5 | by frequency | SNV / small indel | 143 / 438 | 32.65% | 32.03% | 2 / 3 | 32.65–33.33% | E2006K (n=7), G160E (n=4), G1070E (n=4), E886K (n=3), P1005S (n=2) |
| PCDH15 | by frequency | SNV / small indel | 141 / 438 | 32.19% | 31.57% | 2 / 3 | 22.22–32.19% | R764C (n=7), R1522K (n=5), E447K (n=3), R1414Q (n=3), R1273C (n=3) |
| COL4A4 | by frequency | SNV / small indel | 135 / 438 | 30.82% | 30.18% | 2 / 3 | 19.44–30.82% | G757E (n=3), G1204E (n=3), G426W (n=3), P892L (n=3), G1011E (n=3) |
| SCN11A | by frequency | SNV / small indel | 131 / 438 | 29.91% | 29.26% | 2 / 3 | 14.58–29.91% | R1679C (n=4), P1456S (n=3), E923K (n=3), G45E (n=3), E431K (n=3) |
| MROH2B | by frequency | SNV / small indel | 130 / 438 | 29.68% | 29.03% | 2 / 3 | 19.44–29.68% | S1436L (n=6), P173S (n=5), R834W (n=4), D1477N (n=4), E1292K (n=4) |
| UNC13C | by frequency | SNV / small indel | 127 / 438 | 29.0% | 28.57% | 2 / 3 | 20.14–29.0% | E301K (n=4), H2061Y (n=4), E249K (n=3), S1426L (n=3), E1701K (n=3) |
| SPHKAP | by frequency | SNV / small indel | 127 / 438 | 29.0% | 28.34% | 2 / 3 | 22.92–29.0% | E1138K (n=4), E1084K (n=4), G954E (n=4), R285Q (n=3), E1648K (n=3) |
| PTPRT | by frequency | SNV / small indel | 124 / 438 | 28.31% | 27.88% | 3 / 3 | 24.31–36.49% | L695F (n=5), D1285N (n=5), M900I (n=5), E324K (n=5), R328C (n=4) |
| SCN10A | by frequency | SNV / small indel | 121 / 438 | 27.63% | 26.96% | 2 / 3 | 23.61–27.63% | H506Y (n=4), R1782Q (n=4), M374I (n=4), E1239K (n=3), S1820F (n=2) |
| FAM135B | by frequency | SNV / small indel | 121 / 438 | 27.63% | 26.96% | 2 / 3 | 17.36–27.63% | R1211Q (n=3), S1073F (n=3), H92Y (n=3), M1345I (n=3), S657F (n=3) |
| ASXL3 | by frequency | SNV / small indel | 121 / 438 | 27.63% | 26.96% | 2 / 3 | 22.92–27.63% | P1370S (n=10), E453K (n=4), D1725N (n=2), E1645K (n=2), E882K (n=2) |
| SVEP1 | by frequency | SNV / small indel | 119 / 438 | 27.17% | 26.73% | 2 / 3 | 16.67–27.17% | E1165K (n=3), S2365F (n=3), G2786S (n=2), G1320R (n=2), P938L (n=2) |
| ADGRG4 | by frequency | SNV / small indel | 119 / 438 | 27.17% | 26.5% | 2 / 3 | 18.06–27.17% | E873K (n=4), G2695W (n=2), G1557W (n=2), S1414L (n=2), R1086C (n=2) |
| MYH2 | by frequency | SNV / small indel | 118 / 438 | 26.94% | 26.27% | 2 / 3 | 23.61–26.94% | E1382K (n=5), E878K (n=4), P228L (n=3), E347K (n=3), M858I (n=3) |
| GRIN2A | by frequency | SNV / small indel | 118 / 438 | 26.94% | 26.27% | 3 / 3 | 17.36–31.18% | G1322E (n=7), D1153N (n=3), R1067W (n=3), E743K (n=2), D1024N (n=2) |
| RELN | by frequency | SNV / small indel | 117 / 438 | 26.71% | 26.04% | 2 / 3 | 20.14–26.71% | S515F (n=2), W328* (n=2), W2786* (n=2), G804R (n=2), P2345L (n=2) |
| ERICH3 | by frequency | SNV / small indel | 117 / 438 | 26.71% | 26.04% | 2 / 3 | 20.14–26.71% | E1129K (n=3), E773K (n=3), S1524F (n=3), R259C (n=3), P239S (n=2) |
| DCC | by frequency | SNV / small indel | 114 / 438 | 26.03% | 25.35% | 2 / 3 | 22.92–26.03% | R1337* (n=6), R443Q (n=4), R1021* (n=4), G490E (n=4), R501* (n=3) |
| SI | by frequency | SNV / small indel | 113 / 438 | 25.8% | 25.81% | 2 / 3 | 18.75–25.8% | P579S (n=4), W255* (n=3), R157C (n=2), E643K (n=2), R250C (n=2) |
| MYH1 | by frequency | SNV / small indel | 112 / 438 | 25.57% | 24.88% | 2 / 3 | 18.06–25.57% | R791Q (n=6), S1739F (n=5), R24Q (n=4), E1906K (n=3), G1524E (n=3) |
| TACC2 | by frequency | SNV / small indel | 110 / 438 | 25.11% | 24.42% | 2 / 3 | 20.14–25.11% | P2247T (n=3), P781L (n=3), S2397F (n=2), H1486N (n=2), S1920L (n=2) |
| STXBP5L | by frequency | SNV / small indel | 109 / 438 | 24.89% | 24.19% | 2 / 3 | 13.89–24.89% | R696Q (n=4), E320K (n=3), G503E (n=3), R66L (n=2), P397L (n=2) |
| CACNA1E | by frequency | SNV / small indel | 109 / 438 | 24.89% | 24.19% | 2 / 3 | 24.31–24.89% | D1697N (n=4), R2099S (n=3), E1743K (n=3), E462K (n=3), E1690K (n=3) |
| STAB2 | by frequency | SNV / small indel | 108 / 438 | 24.66% | 23.96% | 2 / 3 | 22.92–24.66% | R243Q (n=4), S974L (n=3), G1956E (n=2), S1035F (n=2), G51E (n=2) |
| TRANK1 | by frequency | SNV / small indel | 107 / 438 | 24.43% | 23.73% | 2 / 3 | 23.61–24.43% | E791K (n=3), W2427* (n=3), G2338E (n=3), P2199S (n=3), E1752K (n=3) |
| SCN5A | by frequency | SNV / small indel | 107 / 438 | 24.43% | 23.73% | 2 / 3 | 13.89–24.43% | E431K (n=3), E446K (n=2), E1025K (n=2), G386E (n=2), Q1909* (n=2) |
| NPAP1 | by frequency | SNV / small indel | 107 / 438 | 24.43% | 23.73% | 2 / 3 | 19.44–24.43% | G210E (n=7), S528F (n=5), S887F (n=4), G481R (n=3), D173N (n=2) |
| FCGBP | by frequency | SNV / small indel | 106 / 438 | 24.2% | 23.5% | 2 / 3 | 18.75–24.2% | X5185_splice (n=2), P1427S (n=2), V732I (n=2), R1304Q (n=2), G1482S (n=2) |
| FRAS1 | by frequency | SNV / small indel | 105 / 438 | 23.97% | 23.73% | 2 / 3 | 16.67–23.97% | P1341S (n=2), E3004K (n=2), G2168E (n=2), S1336L (n=2), E2671K (n=2) |
| C6 | by frequency | SNV / small indel | 105 / 438 | 23.97% | 23.27% | 2 / 3 | 18.06–23.97% | R145C (n=6), E871K (n=4), S836F (n=4), S853L (n=3), E170K (n=3) |
| ADAMTS20 | by frequency | SNV / small indel | 105 / 438 | 23.97% | 23.5% | 2 / 3 | 22.22–23.97% | E1019K (n=4), M600I (n=3), S375L (n=3), E1753K (n=3), R359M (n=2) |
| COL7A1 | by frequency | SNV / small indel | 104 / 438 | 23.74% | 23.27% | 2 / 3 | 16.67–23.74% | P1582S (n=3), S430F (n=2), E1923K (n=2), P1410L (n=2), E1535K (n=2) |
| COL3A1 | by frequency | SNV / small indel | 104 / 438 | 23.74% | 23.04% | 2 / 3 | 19.44–23.74% | P80L (n=3), G1014E (n=3), G468R (n=3), P260H (n=3), G609E (n=2) |
| CMYA5 | by frequency | SNV / small indel | 104 / 438 | 23.74% | 23.04% | 2 / 3 | 21.53–23.74% | P478L (n=2), S904L (n=2), P3909H (n=2), E637K (n=2), P2097S (n=2) |
| CD163 | by frequency | SNV / small indel | 104 / 438 | 23.74% | 23.04% | 2 / 3 | 21.53–23.74% | R579K (n=3), S1113F (n=3), G641E (n=3), R584C (n=2), G565E (n=2) |
| TLL1 | by frequency | SNV / small indel | 103 / 438 | 23.52% | 23.04% | 2 / 3 | 15.28–23.52% | Q474* (n=3), E186K (n=3), G220E (n=3), P366S (n=3), R257Q (n=3) |
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 |
|---|---|---|---|---|---|---|---|---|---|
| TCGA PanCancer Atlas cutaneous melanoma (2018) reference | skcm_tcga_pan_can_atlas_2018 | 438 observed | 440 / 448 | exome or genome | WES (440) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 4 | 439.0 |
| MSK-IMPACT melanoma (Clin Cancer Res 2021) | mel_mskimpact_2020 | 696 observed | 696 / 696 | targeted panel | IMPACT468 (437), IMPACT410 (221), IMPACT341 (38) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 4 | 17.0 |
| DFCI metastatic melanoma (Nat Med 2019) | mel_dfci_2019 | 144 observed | 144 / 144 | exome or genome | WES (144) | hg19 | SNV, small indel, amplification, deep deletion | 5 | 246.5 |
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 |
|---|---|---|---|---|---|---|
| CDKN2A | deep deletion | 112 | 367 | 30.52% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| CDKN2A | deep deletion | 180 | 696 | 25.86% | mel_mskimpact_2020 | mel_mskimpact_2020_cna |
| CDKN2A | deep deletion | 32 | 144 | 22.22% | mel_dfci_2019 | mel_dfci_2019_gistic |
| PTEN | deep deletion | 28 | 367 | 7.63% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| MITF | amplification | 24 | 367 | 6.54% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| PTEN | deep deletion | 8 | 144 | 5.56% | mel_dfci_2019 | mel_dfci_2019_gistic |
| TERT | amplification | 19 | 367 | 5.18% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| FAM135B | amplification | 16 | 367 | 4.36% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| FAM135B | amplification | 6 | 144 | 4.17% | mel_dfci_2019 | mel_dfci_2019_gistic |
| BRAF | amplification | 15 | 367 | 4.09% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| PTEN | deep deletion | 27 | 696 | 3.88% | mel_mskimpact_2020 | mel_mskimpact_2020_cna |
| TERT | amplification | 5 | 144 | 3.47% | mel_dfci_2019 | mel_dfci_2019_gistic |
| FCGBP | amplification | 5 | 144 | 3.47% | mel_dfci_2019 | mel_dfci_2019_gistic |
| MITF | amplification | 24 | 696 | 3.45% | mel_mskimpact_2020 | mel_mskimpact_2020_cna |
| MGAM | amplification | 12 | 367 | 3.27% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| NRAS | amplification | 11 | 367 | 3.0% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| KIT | amplification | 4 | 144 | 2.78% | mel_dfci_2019 | mel_dfci_2019_gistic |
| KIT | amplification | 10 | 367 | 2.72% | skcm_tcga_pan_can_atlas_2018 | skcm_tcga_pan_can_atlas_2018_gistic |
| TERT | amplification | 18 | 696 | 2.59% | mel_mskimpact_2020 | mel_mskimpact_2020_cna |
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) |
|---|---|---|
| BRAF | 38.89–53.2% | skcm_tcga_pan_can_atlas_2018: 233/438 (53.2%) · mel_mskimpact_2020: 301/696 (43.25%) · mel_dfci_2019: 56/144 (38.89%) |
| NRAS | 28.54–29.86% | skcm_tcga_pan_can_atlas_2018: 125/438 (28.54%) · mel_mskimpact_2020: 207/696 (29.74%) · mel_dfci_2019: 43/144 (29.86%) |
| NF1 | 17.12–27.87% | skcm_tcga_pan_can_atlas_2018: 75/438 (17.12%) · mel_mskimpact_2020: 194/696 (27.87%) · mel_dfci_2019: 25/144 (17.36%) |
| KIT | 4.86–6.85% | skcm_tcga_pan_can_atlas_2018: 30/438 (6.85%) · mel_mskimpact_2020: 39/696 (5.6%) · mel_dfci_2019: 7/144 (4.86%) |
| MAP2K1 | 6.39–8.48% | skcm_tcga_pan_can_atlas_2018: 28/438 (6.39%) · mel_mskimpact_2020: 59/696 (8.48%) · mel_dfci_2019: 10/144 (6.94%) |
| CDKN2A | 11.81–19.97% | skcm_tcga_pan_can_atlas_2018: 59/438 (13.47%) · mel_mskimpact_2020: 139/696 (19.97%) · mel_dfci_2019: 17/144 (11.81%) |
| PTEN | 7.64–11.78% | skcm_tcga_pan_can_atlas_2018: 43/438 (9.82%) · mel_mskimpact_2020: 82/696 (11.78%) · mel_dfci_2019: 11/144 (7.64%) |
| TERT | 4.11–9.91% | skcm_tcga_pan_can_atlas_2018: 18/438 (4.11%) · mel_mskimpact_2020: 69/696 (9.91%) · mel_dfci_2019: 6/144 (4.17%) |
| PDCD1 | 1.87–3.65% | skcm_tcga_pan_can_atlas_2018: 16/438 (3.65%) · mel_mskimpact_2020: 13/696 (1.87%) · mel_dfci_2019: 4/144 (2.78%) |
| CTLA4 | 1.37–2.78% | skcm_tcga_pan_can_atlas_2018: 6/438 (1.37%) · mel_mskimpact_2020: 16/696 (2.3%) · mel_dfci_2019: 4/144 (2.78%) |
| LAG3 | 2.74–4.86% | skcm_tcga_pan_can_atlas_2018: 12/438 (2.74%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 7/144 (4.86%) |
| MITF | 0.69–2.16% | skcm_tcga_pan_can_atlas_2018: 9/438 (2.05%) · mel_mskimpact_2020: 15/696 (2.16%) · mel_dfci_2019: 1/144 (0.69%) |
| PMEL | 0.69–3.88% | skcm_tcga_pan_can_atlas_2018: 17/438 (3.88%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 1/144 (0.69%) |
| MGAM | 31.25–39.5% | skcm_tcga_pan_can_atlas_2018: 173/438 (39.5%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 45/144 (31.25%) |
| DSCAM | 25.0–34.47% | skcm_tcga_pan_can_atlas_2018: 151/438 (34.47%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 36/144 (25.0%) |
| MXRA5 | 32.65–33.33% | skcm_tcga_pan_can_atlas_2018: 143/438 (32.65%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 48/144 (33.33%) |
| PCDH15 | 22.22–32.19% | skcm_tcga_pan_can_atlas_2018: 141/438 (32.19%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 32/144 (22.22%) |
| COL4A4 | 19.44–30.82% | skcm_tcga_pan_can_atlas_2018: 135/438 (30.82%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 28/144 (19.44%) |
| SCN11A | 14.58–29.91% | skcm_tcga_pan_can_atlas_2018: 131/438 (29.91%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 21/144 (14.58%) |
| MROH2B | 19.44–29.68% | skcm_tcga_pan_can_atlas_2018: 130/438 (29.68%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 28/144 (19.44%) |
| UNC13C | 20.14–29.0% | skcm_tcga_pan_can_atlas_2018: 127/438 (29.0%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 29/144 (20.14%) |
| SPHKAP | 22.92–29.0% | skcm_tcga_pan_can_atlas_2018: 127/438 (29.0%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 33/144 (22.92%) |
| PTPRT | 24.31–36.49% | skcm_tcga_pan_can_atlas_2018: 124/438 (28.31%) · mel_mskimpact_2020: 254/696 (36.49%) · mel_dfci_2019: 35/144 (24.31%) |
| SCN10A | 23.61–27.63% | skcm_tcga_pan_can_atlas_2018: 121/438 (27.63%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 34/144 (23.61%) |
| FAM135B | 17.36–27.63% | skcm_tcga_pan_can_atlas_2018: 121/438 (27.63%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 25/144 (17.36%) |
| ASXL3 | 22.92–27.63% | skcm_tcga_pan_can_atlas_2018: 121/438 (27.63%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 33/144 (22.92%) |
| SVEP1 | 16.67–27.17% | skcm_tcga_pan_can_atlas_2018: 119/438 (27.17%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 24/144 (16.67%) |
| ADGRG4 | 18.06–27.17% | skcm_tcga_pan_can_atlas_2018: 119/438 (27.17%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 26/144 (18.06%) |
| MYH2 | 23.61–26.94% | skcm_tcga_pan_can_atlas_2018: 118/438 (26.94%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 34/144 (23.61%) |
| GRIN2A | 17.36–31.18% | skcm_tcga_pan_can_atlas_2018: 118/438 (26.94%) · mel_mskimpact_2020: 217/696 (31.18%) · mel_dfci_2019: 25/144 (17.36%) |
| RELN | 20.14–26.71% | skcm_tcga_pan_can_atlas_2018: 117/438 (26.71%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 29/144 (20.14%) |
| ERICH3 | 20.14–26.71% | skcm_tcga_pan_can_atlas_2018: 117/438 (26.71%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 29/144 (20.14%) |
| DCC | 22.92–26.03% | skcm_tcga_pan_can_atlas_2018: 114/438 (26.03%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 33/144 (22.92%) |
| SI | 18.75–25.8% | skcm_tcga_pan_can_atlas_2018: 113/438 (25.8%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 27/144 (18.75%) |
| MYH1 | 18.06–25.57% | skcm_tcga_pan_can_atlas_2018: 112/438 (25.57%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 26/144 (18.06%) |
| TACC2 | 20.14–25.11% | skcm_tcga_pan_can_atlas_2018: 110/438 (25.11%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 29/144 (20.14%) |
| STXBP5L | 13.89–24.89% | skcm_tcga_pan_can_atlas_2018: 109/438 (24.89%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 20/144 (13.89%) |
| CACNA1E | 24.31–24.89% | skcm_tcga_pan_can_atlas_2018: 109/438 (24.89%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 35/144 (24.31%) |
| STAB2 | 22.92–24.66% | skcm_tcga_pan_can_atlas_2018: 108/438 (24.66%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 33/144 (22.92%) |
| TRANK1 | 23.61–24.43% | skcm_tcga_pan_can_atlas_2018: 107/438 (24.43%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 34/144 (23.61%) |
| SCN5A | 13.89–24.43% | skcm_tcga_pan_can_atlas_2018: 107/438 (24.43%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 20/144 (13.89%) |
| NPAP1 | 19.44–24.43% | skcm_tcga_pan_can_atlas_2018: 107/438 (24.43%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 28/144 (19.44%) |
| FCGBP | 18.75–24.2% | skcm_tcga_pan_can_atlas_2018: 106/438 (24.2%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 27/144 (18.75%) |
| FRAS1 | 16.67–23.97% | skcm_tcga_pan_can_atlas_2018: 105/438 (23.97%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 24/144 (16.67%) |
| C6 | 18.06–23.97% | skcm_tcga_pan_can_atlas_2018: 105/438 (23.97%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 26/144 (18.06%) |
| ADAMTS20 | 22.22–23.97% | skcm_tcga_pan_can_atlas_2018: 105/438 (23.97%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 32/144 (22.22%) |
| COL7A1 | 16.67–23.74% | skcm_tcga_pan_can_atlas_2018: 104/438 (23.74%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 24/144 (16.67%) |
| COL3A1 | 19.44–23.74% | skcm_tcga_pan_can_atlas_2018: 104/438 (23.74%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 28/144 (19.44%) |
| CMYA5 | 21.53–23.74% | skcm_tcga_pan_can_atlas_2018: 104/438 (23.74%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 31/144 (21.53%) |
| CD163 | 21.53–23.74% | skcm_tcga_pan_can_atlas_2018: 104/438 (23.74%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 31/144 (21.53%) |
| TLL1 | 15.28–23.52% | skcm_tcga_pan_can_atlas_2018: 103/438 (23.52%) · mel_mskimpact_2020: not assayed · mel_dfci_2019: 22/144 (15.28%) |
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 2026-09-17; 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/melanoma.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.