Disease intelligence · mutation landscape
Glioblastoma mutation landscape
How often each gene is altered in glioblastoma, 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 glioblastoma (2018) (390 sequenced patients, exome or genome), the most frequently altered of the 45 genes shown are CDKN2A 56.0% (deep deletion), EGFR 44.35% (amplification), PTEN 32.82%, TP53 30.77%, CDK4 14.26% (amplification). Each figure divides by the patients on whom that gene could be called.
6 of 390 patients are hypermutated (more than 510 non-silent mutations, ten times the cohort median of 51); every gene's frequency without them is beside the headline.
Of the briefing's 12 curated targets, 2 are altered in under 2% of this cohort (TERT, MGMT): 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 | gbm_tcga_pan_can_atlas_2018 390 pts · exome or genome | gbm_cptac_2021 99 pts · exome or genome | gbm_columbia_2019 32 pts · exome or genome |
|---|---|---|---|
| EGFR SNV / small indel | 23.33%91/390 | 17.17%17/99 | 3.12%1/32 |
| EGFR amplification | 44.35%255/575 | 48.96%47/96 | · |
| PDGFRA SNV / small indel | 4.1%16/390 | 3.03%3/99 | 0% |
| PDGFRA amplification | 13.04%75/575 | 12.5%12/96 | · |
| PTEN SNV / small indel | 32.82%128/390 | 27.27%27/99 | 15.62%5/32 |
| PTEN deep deletion | 9.57%55/575 | 12.5%12/96 | · |
| TP53 SNV / small indel | 30.77%120/390 | 32.32%32/99 | 9.38%3/32 |
| NF1 SNV / small indel | 11.79%46/390 | 15.15%15/99 | 9.38%3/32 |
| NF1 deep deletion | 1.57%9/575 | 4.17%4/96 | · |
| CDK4 SNV / small indel | 0% | 0% | 0% |
| CDK4 amplification | 14.26%82/575 | 14.58%14/96 | · |
| MDM2 SNV / small indel | 0.77%3/390 | 2.02%2/99 | 0% |
| MDM2 amplification | 8.17%47/575 | 7.29%7/96 | · |
| CDKN2A SNV / small indel | 1.03%4/390 | 1.01%1/99 | 0% |
| CDKN2A deep deletion | 56.0%322/575 | 58.33%56/96 | · |
| RB1 SNV / small indel | 9.74%38/390 | 10.1%10/99 | 3.12%1/32 |
| RB1 deep deletion | 2.61%15/575 | 4.17%4/96 | · |
| PIK3CA SNV / small indel | 9.23%36/390 | 11.11%11/99 | 9.38%3/32 |
| PIK3CA amplification | 2.78%16/575 | 3.12%3/96 | · |
| TERT SNV / small indel | 1.28%5/390 | 1.01%1/99 | 0% |
| TERT amplification | 0.7%4/575 | 3.12%3/96 | · |
| MGMT SNV / small indel | 0.77%3/390 | 0% | 0% |
| MGMT deep deletion | 0.17%1/575 | 3.12%3/96 | · |
| PIK3R1 SNV / small indel | 10.0%39/390 | 7.07%7/99 | 0% |
| ATRX SNV / small indel | 9.23%36/390 | 10.1%10/99 | 3.12%1/32 |
| PKHD1 SNV / small indel | 6.67%26/390 | 5.05%5/99 | 6.25%2/32 |
| COL6A3 SNV / small indel | 6.41%25/390 | 1.01%1/99 | 0% |
| IDH1 SNV / small indel | 6.15%24/390 | 7.07%7/99 | 12.5%4/32 |
| HRNR SNV / small indel | 5.38%21/390 | 3.03%3/99 | 0% |
| FAT2 SNV / small indel | 5.38%21/390 | 1.01%1/99 | 6.25%2/32 |
| RELN SNV / small indel | 5.13%20/390 | 1.01%1/99 | 3.12%1/32 |
| LAMA1 SNV / small indel | 5.13%20/390 | 0% | 3.12%1/32 |
| CFAP47 SNV / small indel | 5.13%20/390 | 2.02%2/99 | 0% |
| RIMS2 SNV / small indel | 4.87%19/390 | 1.01%1/99 | 0% |
| KMT2C SNV / small indel | 4.87%19/390 | 4.04%4/99 | 0% |
| KMT2C amplification | 2.26%13/575 | 1.04%1/96 | · |
| CNTNAP2 SNV / small indel | 4.87%19/390 | 3.03%3/99 | 0% |
| CNTNAP2 amplification | 2.43%14/575 | 2.08%2/96 | · |
| TCHH SNV / small indel | 4.62%18/390 | 0% | 0% |
| STAG2 SNV / small indel | 4.62%18/390 | 1.01%1/99 | 0% |
| SDK1 SNV / small indel | 4.62%18/390 | 1.01%1/99 | 3.12%1/32 |
| KEL SNV / small indel | 4.62%18/390 | 2.02%2/99 | 0% |
| KEL amplification | 1.39%8/575 | 2.08%2/96 | · |
| HSPG2 SNV / small indel | 4.62%18/390 | 0% | 0% |
| MXRA5 SNV / small indel | 4.36%17/390 | 5.05%5/99 | 0% |
| MXRA5 amplification | 0.17%1/575 | 2.08%2/96 | · |
| LZTR1 SNV / small indel | 4.36%17/390 | 1.01%1/99 | 0% |
| GALNT17 SNV / small indel | 4.36%17/390 | 2.02%2/99 | 0% |
| GALNT17 amplification | 1.57%9/575 | 2.08%2/96 | · |
| DOCK5 SNV / small indel | 4.36%17/390 | 1.01%1/99 | 0% |
| TAF1L SNV / small indel | 4.1%16/390 | 2.02%2/99 | 0% |
| SCN9A SNV / small indel | 4.1%16/390 | 2.02%2/99 | 0% |
| MROH2B SNV / small indel | 4.1%16/390 | 2.02%2/99 | 0% |
| KIF2B SNV / small indel | 4.1%16/390 | 1.01%1/99 | 3.12%1/32 |
| FRAS1 SNV / small indel | 4.1%16/390 | 5.05%5/99 | 3.12%1/32 |
| FBN3 SNV / small indel | 4.1%16/390 | 4.04%4/99 | 0% |
| DSP SNV / small indel | 4.1%16/390 | 1.01%1/99 | 0% |
| SLIT3 SNV / small indel | 3.85%15/390 | 1.01%1/99 | 0% |
| PIK3CG SNV / small indel | 3.85%15/390 | 1.01%1/99 | 0% |
| GRIN2A SNV / small indel | 3.85%15/390 | 1.01%1/99 | 0% |
| FCGBP SNV / small indel | 3.85%15/390 | 0% | 0% |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
CDKN2A is deleted in 322 of 575 patients in TCGA PanCancer Atlas glioblastoma (2018).
EGFR is amplified in 255 of 575 patients in TCGA PanCancer Atlas glioblastoma (2018).
PTEN is mutated in 128 of 390 patients in TCGA PanCancer Atlas glioblastoma (2018).
Gene table — reference cohort
Headline values are from the reference cohort, gbm_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.
FDA biomarker marks a gene the FDA recognises as a biomarker of response to an approved drug; FDA, tumour-agnostic marks the five that apply whatever the primary site. Hover for the drug, the tumour type and the year. This is level 1 only, United States only, and frozen at November 2022 — a dash means the gene was not FDA-recognised on that date, not that it is undruggable, and not that no trial exists. The frequency beside it is how often the gene is altered in this disease, which is a different question from whether these patients are eligible for the drug. Source: Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer. Cancer Discovery 2024;14(1):49-65. doi:10.1158/2159-8290.CD-23-0467, Table 1
| Gene | FDA status | Why listed | Largest alteration | Altered / tested | Frequency | Without hypermutated | Cohorts observed | Range across cohorts | Recurrent changes |
|---|---|---|---|---|---|---|---|---|---|
| EGFR | FDA biomarker2004 · 7 drugs | curated target | amplification | 255 / 575 | 44.35% mutation 23.33% | 22.92% | 3 / 3 | 3.12–23.33% | A289V (n=16), G598V (n=15), R222C (n=6), A289T (n=6), A289D (n=5) |
| PDGFRA | FDA biomarker2006 · 2 drugs | curated target | amplification | 75 / 575 | 13.04% mutation 4.1% | 3.65% | 2 / 3 | 0.0–4.1% | E229K (n=2), W349C (n=1), P1021L (n=1), E372K (n=1), L655F (n=1) |
| PTEN | — | curated target | SNV / small indel | 128 / 390 | 32.82% | 32.55% | 3 / 3 | 15.62–32.82% | R233* (n=5), T319* (n=5), G132D (n=4), R335* (n=3), R173H (n=3) |
| TP53 | — | curated target | SNV / small indel | 120 / 390 | 30.77% | 30.21% | 3 / 3 | 9.38–32.32% | R248Q (n=8), R175H (n=8), R282W (n=5), Y220C (n=5), R248W (n=5) |
| NF1 | FDA biomarker2020 · 1 drug | curated target | SNV / small indel | 46 / 390 | 11.79% | 10.94% | 3 / 3 | 9.38–15.15% | K1661Gfs*36 (n=3), R192* (n=2), X2657_splice (n=2), X1445_splice (n=1), L844F (n=1) |
| CDK4 | — | curated target | amplification | 82 / 575 | 14.26% mutation 0.0% | 0.0% | 0 / 3 | 0.0–0.0% | none recurrent |
| MDM2 | — | curated target | amplification | 47 / 575 | 8.17% mutation 0.77% | 0.26% | 2 / 3 | 0.0–2.02% | D86Y (n=1), S127F (n=1), I303M (n=1) |
| CDKN2A | — | curated target | deep deletion | 322 / 575 | 56.0% mutation 1.03% | 0.78% | 2 / 3 | 0.0–1.03% | W110* (n=2), L78Hfs*41 (n=1), G111D (n=1) |
| RB1 | — | curated target | SNV / small indel | 38 / 390 | 9.74% | 8.85% | 3 / 3 | 3.12–10.1% | R445* (n=3), X830_splice (n=2), X654_splice (n=2), S318Nfs*13 (n=2), Q702* (n=1) |
| PIK3CA | FDA biomarker2019 · 1 drug | curated target | SNV / small indel | 36 / 390 | 9.23% | 8.85% | 3 / 3 | 9.23–11.11% | M1043V (n=3), E545K (n=3), R38H (n=2), E81K (n=2), R88Q (n=2) |
| TERT | — | curated target | SNV / small indel | 5 / 390 | 1.28% | 0.78% | 2 / 3 | 0.0–1.28% | G641* (n=1), P219L (n=1), N571S (n=1), R889Q (n=1), R951Q (n=1) |
| MGMT | — | curated target | SNV / small indel | 3 / 390 | 0.77% | 0.26% | 1 / 3 | 0.0–0.77% | A82V (n=1), V186M (n=1), A226V (n=1) |
| PIK3R1 | — | by frequency | SNV / small indel | 39 / 390 | 10.0% | 9.64% | 2 / 3 | 0.0–10.0% | G376R (n=6), X582_splice (n=2), K379N (n=2), X583_splice (n=2), R574Kfs*27 (n=1) |
| ATRX | — | by frequency | SNV / small indel | 36 / 390 | 9.23% | 8.07% | 3 / 3 | 3.12–10.1% | Q177* (n=2), R1803H (n=2), W2001Cfs*14 (n=1), E886Lfs*18 (n=1), L1827Cfs*9 (n=1) |
| PKHD1 | — | by frequency | SNV / small indel | 26 / 390 | 6.67% | 6.25% | 3 / 3 | 5.05–6.67% | L1989F (n=2), R1624W (n=1), F2516S (n=1), G3676E (n=1), T849N (n=1) |
| COL6A3 | — | by frequency | SNV / small indel | 25 / 390 | 6.41% | 5.99% | 2 / 3 | 0.0–6.41% | S2492L (n=2), L1723F (n=1), V987M (n=1), A1094T (n=1), G542S (n=1) |
| IDH1 | FDA biomarker2018 · 1 drug | by frequency | SNV / small indel | 24 / 390 | 6.15% | 6.25% | 3 / 3 | 6.15–12.5% | R132H (n=22), R132G (n=2), R132C (n=1) |
| HRNR | — | by frequency | SNV / small indel | 21 / 390 | 5.38% | 4.95% | 2 / 3 | 0.0–5.38% | S245T (n=2), S2035G (n=1), R571H (n=1), R1053* (n=1), S316L (n=1) |
| FAT2 | — | by frequency | SNV / small indel | 21 / 390 | 5.38% | 4.95% | 3 / 3 | 1.01–6.25% | T3563M (n=2), R2117Q (n=1), P2269T (n=1), V3619M (n=1), Y2911* (n=1) |
| RELN | — | by frequency | SNV / small indel | 20 / 390 | 5.13% | 4.17% | 3 / 3 | 1.01–5.13% | D365N (n=1), N1761S (n=1), Q176* (n=1), R3018* (n=1), A2036V (n=1) |
| LAMA1 | — | by frequency | SNV / small indel | 20 / 390 | 5.13% | 4.17% | 2 / 3 | 0.0–5.13% | X256_splice (n=1), R1180H (n=1), S1051L (n=1), F2643L (n=1), E844K (n=1) |
| CFAP47 | — | by frequency | SNV / small indel | 20 / 390 | 5.13% | 4.95% | 2 / 3 | 0.0–5.13% | I324N (n=2), R554H (n=2), D304Y (n=1), K257I (n=1), R458I (n=1) |
| RIMS2 | — | by frequency | SNV / small indel | 19 / 390 | 4.87% | 4.43% | 2 / 3 | 0.0–4.87% | R1003H (n=2), R977Q (n=2), R998* (n=2), S511L (n=1), R683* (n=1) |
| KMT2C | — | by frequency | SNV / small indel | 19 / 390 | 4.87% | 4.17% | 2 / 3 | 0.0–4.87% | K395E (n=1), D2714H (n=1), G964V (n=1), N2339K (n=1), E4271G (n=1) |
| CNTNAP2 | — | by frequency | SNV / small indel | 19 / 390 | 4.87% | 4.43% | 2 / 3 | 0.0–4.87% | R283H (n=1), R483Q (n=1), R1032I (n=1), F689L (n=1), F1281L (n=1) |
| TCHH | — | by frequency | SNV / small indel | 18 / 390 | 4.62% | 4.17% | 1 / 3 | 0.0–4.62% | R233Q (n=1), P978L (n=1), P265L (n=1), R1111W (n=1), R1483H (n=1) |
| STAG2 | — | by frequency | SNV / small indel | 18 / 390 | 4.62% | 4.43% | 2 / 3 | 0.0–4.62% | M803Vfs*5 (n=1), E675D (n=1), E6* (n=1), L791M (n=1), Y815* (n=1) |
| SDK1 | — | by frequency | SNV / small indel | 18 / 390 | 4.62% | 4.17% | 3 / 3 | 1.01–4.62% | S1074P (n=1), P972S (n=1), V1229I (n=1), S1208F (n=1), G929E (n=1) |
| KEL | — | by frequency | SNV / small indel | 18 / 390 | 4.62% | 4.43% | 2 / 3 | 0.0–4.62% | X75_splice (n=2), R130W (n=2), V411M (n=2), V336M (n=1), S187Y (n=1) |
| HSPG2 | — | by frequency | SNV / small indel | 18 / 390 | 4.62% | 3.65% | 1 / 3 | 0.0–4.62% | R187* (n=1), G759S (n=1), G3637D (n=1), P1449A (n=1), A1410V (n=1) |
| MXRA5 | — | by frequency | SNV / small indel | 17 / 390 | 4.36% | 3.65% | 2 / 3 | 0.0–5.05% | R2119H (n=1), I1326T (n=1), V2022I (n=1), R1280K (n=1), L602V (n=1) |
| LZTR1 | — | by frequency | SNV / small indel | 17 / 390 | 4.36% | 3.65% | 2 / 3 | 0.0–4.36% | R810W (n=1), W105R (n=1), G248R (n=1), C560R (n=1), L591R (n=1) |
| GALNT17 | — | by frequency | SNV / small indel | 17 / 390 | 4.36% | 3.39% | 2 / 3 | 0.0–4.36% | V544I (n=2), E485V (n=1), A46T (n=1), K200R (n=1), K382* (n=1) |
| DOCK5 | — | by frequency | SNV / small indel | 17 / 390 | 4.36% | 3.65% | 2 / 3 | 0.0–4.36% | R211W (n=2), T282R (n=1), R1019H (n=1), V715I (n=1), G408S (n=1) |
| TAF1L | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.39% | 2 / 3 | 0.0–4.1% | T1673R (n=1), R1252W (n=1), D1667N (n=1), D6N (n=1), A1430T (n=1) |
| SCN9A | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.91% | 2 / 3 | 0.0–4.1% | D1828Y (n=1), N1353Y (n=1), R1368H (n=1), R1903P (n=1), T1633M (n=1) |
| MROH2B | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.65% | 2 / 3 | 0.0–4.1% | R181* (n=2), T456N (n=1), R54* (n=1), R390Q (n=1), P554L (n=1) |
| KIF2B | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.65% | 3 / 3 | 1.01–4.1% | A112T (n=1), E378Rfs*24 (n=1), E62D (n=1), K143N (n=1), R160W (n=1) |
| FRAS1 | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.65% | 3 / 3 | 3.12–5.05% | H1855N (n=1), R1891H (n=1), T2578I (n=1), A3021V (n=1), R3768H (n=1) |
| FBN3 | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.91% | 2 / 3 | 0.0–4.1% | V886I (n=2), A1730T (n=1), R2108C (n=1), P2396Q (n=1), V697M (n=1) |
| DSP | — | by frequency | SNV / small indel | 16 / 390 | 4.1% | 3.12% | 2 / 3 | 0.0–4.1% | R270Q (n=2), X1793_splice (n=1), T496M (n=1), S610F (n=1), K441T (n=1) |
| SLIT3 | — | by frequency | SNV / small indel | 15 / 390 | 3.85% | 2.86% | 2 / 3 | 0.0–3.85% | V596M (n=2), R744C (n=1), A1174T (n=1), D1370N (n=1), R469* (n=1) |
| PIK3CG | — | by frequency | SNV / small indel | 15 / 390 | 3.85% | 2.86% | 2 / 3 | 0.0–3.85% | V165I (n=2), C936S (n=1), A156V (n=1), D571Y (n=1), P424S (n=1) |
| GRIN2A | — | by frequency | SNV / small indel | 15 / 390 | 3.85% | 3.39% | 2 / 3 | 0.0–3.85% | T1064M (n=1), Q891R (n=1), W7* (n=1), F253L (n=1), C399R (n=1) |
| FCGBP | — | by frequency | SNV / small indel | 15 / 390 | 3.85% | 3.39% | 1 / 3 | 0.0–3.85% | R4260P (n=1), G1100D (n=1), R434Q (n=1), C2688S (n=1), L1464I (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 |
|---|---|---|---|---|---|---|---|---|---|
| TCGA PanCancer Atlas glioblastoma (2018) reference | gbm_tcga_pan_can_atlas_2018 | 390 observed | 397 / 592 | exome or genome | WES (397) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 6 | 51 |
| CPTAC glioblastoma (Cell 2021) | gbm_cptac_2021 | 99 observed | 99 / 99 | exome or genome | WES (99) | hg19 | SNV, small indel, amplification, deep deletion | 1 | 42 |
| Columbia glioblastoma (Nat Med 2019) | gbm_columbia_2019 | 32 observed | 32 / 42 | exome or genome | WES (32) | hg19 | SNV, small indel | 0 | 0.0 |
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 | 56 | 96 | 58.33% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| CDKN2A | deep deletion | 322 | 575 | 56.0% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| EGFR | amplification | 47 | 96 | 48.96% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| EGFR | amplification | 255 | 575 | 44.35% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| CDK4 | amplification | 14 | 96 | 14.58% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| CDK4 | amplification | 82 | 575 | 14.26% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| PDGFRA | amplification | 75 | 575 | 13.04% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| PDGFRA | amplification | 12 | 96 | 12.5% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| PTEN | deep deletion | 12 | 96 | 12.5% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| PTEN | deep deletion | 55 | 575 | 9.57% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| MDM2 | amplification | 47 | 575 | 8.17% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| MDM2 | amplification | 7 | 96 | 7.29% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| NF1 | deep deletion | 4 | 96 | 4.17% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| RB1 | deep deletion | 4 | 96 | 4.17% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| PIK3CA | amplification | 3 | 96 | 3.12% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| TERT | amplification | 3 | 96 | 3.12% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| MGMT | deep deletion | 3 | 96 | 3.12% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| PIK3CA | amplification | 16 | 575 | 2.78% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 15 | 575 | 2.61% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| CNTNAP2 | amplification | 14 | 575 | 2.43% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| KMT2C | amplification | 13 | 575 | 2.26% | gbm_tcga_pan_can_atlas_2018 | gbm_tcga_pan_can_atlas_2018_gistic |
| CNTNAP2 | amplification | 2 | 96 | 2.08% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| KEL | amplification | 2 | 96 | 2.08% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| MXRA5 | amplification | 2 | 96 | 2.08% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
| GALNT17 | amplification | 2 | 96 | 2.08% | gbm_cptac_2021 | gbm_cptac_2021_gistic |
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) |
|---|---|---|
| EGFR | 3.12–23.33% | gbm_tcga_pan_can_atlas_2018: 91/390 (23.33%) · gbm_cptac_2021: 17/99 (17.17%) · gbm_columbia_2019: 1/32 (3.12%) |
| PDGFRA | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 3/99 (3.03%) · gbm_columbia_2019: 0/32 (0.0%) |
| PTEN | 15.62–32.82% | gbm_tcga_pan_can_atlas_2018: 128/390 (32.82%) · gbm_cptac_2021: 27/99 (27.27%) · gbm_columbia_2019: 5/32 (15.62%) |
| TP53 | 9.38–32.32% | gbm_tcga_pan_can_atlas_2018: 120/390 (30.77%) · gbm_cptac_2021: 32/99 (32.32%) · gbm_columbia_2019: 3/32 (9.38%) |
| NF1 | 9.38–15.15% | gbm_tcga_pan_can_atlas_2018: 46/390 (11.79%) · gbm_cptac_2021: 15/99 (15.15%) · gbm_columbia_2019: 3/32 (9.38%) |
| CDK4 | 0.0–0.0% | gbm_tcga_pan_can_atlas_2018: 0/390 (0.0%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 0/32 (0.0%) |
| MDM2 | 0.0–2.02% | gbm_tcga_pan_can_atlas_2018: 3/390 (0.77%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| CDKN2A | 0.0–1.03% | gbm_tcga_pan_can_atlas_2018: 4/390 (1.03%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| RB1 | 3.12–10.1% | gbm_tcga_pan_can_atlas_2018: 38/390 (9.74%) · gbm_cptac_2021: 10/99 (10.1%) · gbm_columbia_2019: 1/32 (3.12%) |
| PIK3CA | 9.23–11.11% | gbm_tcga_pan_can_atlas_2018: 36/390 (9.23%) · gbm_cptac_2021: 11/99 (11.11%) · gbm_columbia_2019: 3/32 (9.38%) |
| TERT | 0.0–1.28% | gbm_tcga_pan_can_atlas_2018: 5/390 (1.28%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| MGMT | 0.0–0.77% | gbm_tcga_pan_can_atlas_2018: 3/390 (0.77%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 0/32 (0.0%) |
| PIK3R1 | 0.0–10.0% | gbm_tcga_pan_can_atlas_2018: 39/390 (10.0%) · gbm_cptac_2021: 7/99 (7.07%) · gbm_columbia_2019: 0/32 (0.0%) |
| ATRX | 3.12–10.1% | gbm_tcga_pan_can_atlas_2018: 36/390 (9.23%) · gbm_cptac_2021: 10/99 (10.1%) · gbm_columbia_2019: 1/32 (3.12%) |
| PKHD1 | 5.05–6.67% | gbm_tcga_pan_can_atlas_2018: 26/390 (6.67%) · gbm_cptac_2021: 5/99 (5.05%) · gbm_columbia_2019: 2/32 (6.25%) |
| COL6A3 | 0.0–6.41% | gbm_tcga_pan_can_atlas_2018: 25/390 (6.41%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| IDH1 | 6.15–12.5% | gbm_tcga_pan_can_atlas_2018: 24/390 (6.15%) · gbm_cptac_2021: 7/99 (7.07%) · gbm_columbia_2019: 4/32 (12.5%) |
| HRNR | 0.0–5.38% | gbm_tcga_pan_can_atlas_2018: 21/390 (5.38%) · gbm_cptac_2021: 3/99 (3.03%) · gbm_columbia_2019: 0/32 (0.0%) |
| FAT2 | 1.01–6.25% | gbm_tcga_pan_can_atlas_2018: 21/390 (5.38%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 2/32 (6.25%) |
| RELN | 1.01–5.13% | gbm_tcga_pan_can_atlas_2018: 20/390 (5.13%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 1/32 (3.12%) |
| LAMA1 | 0.0–5.13% | gbm_tcga_pan_can_atlas_2018: 20/390 (5.13%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 1/32 (3.12%) |
| CFAP47 | 0.0–5.13% | gbm_tcga_pan_can_atlas_2018: 20/390 (5.13%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| RIMS2 | 0.0–4.87% | gbm_tcga_pan_can_atlas_2018: 19/390 (4.87%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| KMT2C | 0.0–4.87% | gbm_tcga_pan_can_atlas_2018: 19/390 (4.87%) · gbm_cptac_2021: 4/99 (4.04%) · gbm_columbia_2019: 0/32 (0.0%) |
| CNTNAP2 | 0.0–4.87% | gbm_tcga_pan_can_atlas_2018: 19/390 (4.87%) · gbm_cptac_2021: 3/99 (3.03%) · gbm_columbia_2019: 0/32 (0.0%) |
| TCHH | 0.0–4.62% | gbm_tcga_pan_can_atlas_2018: 18/390 (4.62%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 0/32 (0.0%) |
| STAG2 | 0.0–4.62% | gbm_tcga_pan_can_atlas_2018: 18/390 (4.62%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| SDK1 | 1.01–4.62% | gbm_tcga_pan_can_atlas_2018: 18/390 (4.62%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 1/32 (3.12%) |
| KEL | 0.0–4.62% | gbm_tcga_pan_can_atlas_2018: 18/390 (4.62%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| HSPG2 | 0.0–4.62% | gbm_tcga_pan_can_atlas_2018: 18/390 (4.62%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 0/32 (0.0%) |
| MXRA5 | 0.0–5.05% | gbm_tcga_pan_can_atlas_2018: 17/390 (4.36%) · gbm_cptac_2021: 5/99 (5.05%) · gbm_columbia_2019: 0/32 (0.0%) |
| LZTR1 | 0.0–4.36% | gbm_tcga_pan_can_atlas_2018: 17/390 (4.36%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| GALNT17 | 0.0–4.36% | gbm_tcga_pan_can_atlas_2018: 17/390 (4.36%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| DOCK5 | 0.0–4.36% | gbm_tcga_pan_can_atlas_2018: 17/390 (4.36%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| TAF1L | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| SCN9A | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| MROH2B | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 2/99 (2.02%) · gbm_columbia_2019: 0/32 (0.0%) |
| KIF2B | 1.01–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 1/32 (3.12%) |
| FRAS1 | 3.12–5.05% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 5/99 (5.05%) · gbm_columbia_2019: 1/32 (3.12%) |
| FBN3 | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 4/99 (4.04%) · gbm_columbia_2019: 0/32 (0.0%) |
| DSP | 0.0–4.1% | gbm_tcga_pan_can_atlas_2018: 16/390 (4.1%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| SLIT3 | 0.0–3.85% | gbm_tcga_pan_can_atlas_2018: 15/390 (3.85%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| PIK3CG | 0.0–3.85% | gbm_tcga_pan_can_atlas_2018: 15/390 (3.85%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| GRIN2A | 0.0–3.85% | gbm_tcga_pan_can_atlas_2018: 15/390 (3.85%) · gbm_cptac_2021: 1/99 (1.01%) · gbm_columbia_2019: 0/32 (0.0%) |
| FCGBP | 0.0–3.85% | gbm_tcga_pan_can_atlas_2018: 15/390 (3.85%) · gbm_cptac_2021: 0/99 (0.0%) · gbm_columbia_2019: 0/32 (0.0%) |
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 2026-09-28; 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.
- Promoter mutations are a separate row. A cohort that reports none is marked not assayed, not zero: whole-exome studies such as the TCGA pan-cancer atlas do not cover the TERT promoter, so a low coding-only TERT figure there is not a low TERT rate.
- 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/glioblastoma.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.