Disease intelligence · mutation landscape
Gallbladder cancer mutation landscape
How often each gene is altered in gallbladder cancer, 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 Gallbladder Cancer (MSK, 2022) (233 sequenced patients, targeted panel), the most frequently altered of the 43 genes shown are TP53 63.95%, SMAD4 21.89%, ARID1A 20.6%, CDKN2A 15.02% (deep deletion), ELF3 10.75%. 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 (FGFR2, IDH1): 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 | gbc_mskcc_2022 233 pts · targeted panel | gbc_shanghai_2014 32 pts · exome or genome |
|---|---|---|
| ERBB2 SNV / small indel | 7.3%17/233 | 9.38%3/32 |
| ERBB2 amplification | 10.3%24/233 | · |
| TP53 SNV / small indel | 63.95%149/233 | 25.0%8/32 |
| KRAS SNV / small indel | 7.73%18/233 | 0% |
| KRAS amplification | 4.29%10/233 | · |
| PIK3CA SNV / small indel | 10.73%25/233 | 6.25%2/32 |
| CDKN2A SNV / small indel | 9.87%23/233 | 0% |
| CDKN2A deep deletion | 15.02%35/233 | · |
| ARID1A SNV / small indel | 20.6%48/233 | 6.25%2/32 |
| ERBB3 SNV / small indel | 6.44%15/233 | 9.38%3/32 |
| ERBB3 amplification | 5.15%12/233 | · |
| EGFR SNV / small indel | 1.29%3/233 | 3.12%1/32 |
| EGFR amplification | 3.43%8/233 | · |
| CTNNB1 SNV / small indel | 6.44%15/233 | 0% |
| SMAD4 SNV / small indel | 21.89%51/233 | 3.12%1/32 |
| SMAD4 deep deletion | 4.72%11/233 | · |
| FGFR2 SNV / small indel | 1.29%3/233 | 0% |
| IDH1 SNV / small indel | 0.43%1/233 | 0% |
| STK11 SNV / small indel | 9.44%22/233 | 0% |
| KMT2C SNV / small indel | 8.58%20/233 | 9.38%3/32 |
| ELF3 SNV / small indel | 10.75%20/186 | 6.25%2/32 |
| ARID2 SNV / small indel | 8.58%20/233 | 6.25%2/32 |
| KMT2D SNV / small indel | 6.87%16/233 | 3.12%1/32 |
| ATM SNV / small indel | 6.87%16/233 | 3.12%1/32 |
| BRCA2 SNV / small indel | 5.58%13/233 | 0% |
| RBM10 SNV / small indel | 4.72%11/233 | 0% |
| RB1 SNV / small indel | 4.29%10/233 | 3.12%1/32 |
| RB1 deep deletion | 3.0%7/233 | · |
| PBRM1 SNV / small indel | 4.29%10/233 | 0% |
| NF1 SNV / small indel | 4.29%10/233 | 0% |
| KMT2A SNV / small indel | 4.29%10/233 | 0% |
| SLX4 SNV / small indel | 4.84%9/186 | 3.12%1/32 |
| PREX2 SNV / small indel | 4.84%9/186 | 3.12%1/32 |
| KEAP1 SNV / small indel | 3.86%9/233 | 0% |
| FBXW7 SNV / small indel | 3.86%9/233 | 3.12%1/32 |
| AXIN1 SNV / small indel | 3.86%9/233 | 0% |
| ATRX SNV / small indel | 3.86%9/233 | 3.12%1/32 |
| RASA1 SNV / small indel | 3.43%8/233 | 0% |
| PTPRD SNV / small indel | 3.43%8/233 | 0% |
| NOTCH3 SNV / small indel | 3.43%8/233 | 0% |
| JAK1 SNV / small indel | 3.43%8/233 | 0% |
| IKZF1 SNV / small indel | 3.43%8/233 | 0% |
| EP300 SNV / small indel | 3.43%8/233 | 0% |
| CDK12 SNV / small indel | 3.43%8/233 | 0% |
| CDK12 amplification | 6.87%16/233 | · |
| ARID1B SNV / small indel | 3.43%8/233 | 0% |
| ARID1B deep deletion | 2.15%5/233 | · |
| APC SNV / small indel | 3.43%8/233 | 0% |
| ZFHX3 SNV / small indel | 3.11%7/225 | 0% |
| RNF43 SNV / small indel | 3.0%7/233 | 0% |
| PTPRS SNV / small indel | 3.0%7/233 | 3.12%1/32 |
| PTEN SNV / small indel | 3.0%7/233 | 0% |
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 149 of 233 patients in Gallbladder Cancer (MSK, 2022).
SMAD4 is mutated in 51 of 233 patients in Gallbladder Cancer (MSK, 2022).
ARID1A is mutated in 48 of 233 patients in Gallbladder Cancer (MSK, 2022).
Gene table — reference cohort
Headline values are from the reference cohort, gbc_mskcc_2022; 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 |
|---|---|---|---|---|---|---|---|---|---|
| ERBB2 | FDA biomarker1998 · 9 drugs | curated target | amplification | 24 / 233 | 10.3% mutation 7.3% | — | 2 / 2 | 7.3–9.38% | S310F (n=5), S310Y (n=5), D769Y (n=3), L755S (n=2), R678Q (n=2) |
| TP53 | — | curated target | SNV / small indel | 149 / 233 | 63.95% | — | 2 / 2 | 25.0–63.95% | R248Q (n=9), R175H (n=7), R273H (n=5), Y234C (n=4), R306* (n=3) |
| KRAS | FDA, wild-type2009 · 3 drugs | curated target | SNV / small indel | 18 / 233 | 7.73% | — | 1 / 2 | 0.0–7.73% | G13D (n=5), G12D (n=5), Q61H (n=2), G12C (n=2), G12A (n=2) |
| PIK3CA | FDA biomarker2019 · 1 drug | curated target | SNV / small indel | 25 / 233 | 10.73% | — | 2 / 2 | 6.25–10.73% | E542K (n=6), E545K (n=4), H1047R (n=4), E81K (n=2), E726K (n=2) |
| CDKN2A | — | curated target | deep deletion | 35 / 233 | 15.02% mutation 9.87% | — | 1 / 2 | 0.0–9.87% | R80* (n=3), R29_A34del (n=2), D84N (n=2), E120* (n=2), E10* (n=2) |
| ARID1A | — | curated target | SNV / small indel | 48 / 233 | 20.6% | — | 2 / 2 | 6.25–20.6% | Y551Lfs*72 (n=2), D322Y (n=2), Q1095del (n=2), Q515* (n=2), A1978Sfs*36 (n=1) |
| ERBB3 | — | curated target | SNV / small indel | 15 / 233 | 6.44% | — | 2 / 2 | 6.44–9.38% | T355I (n=2), G914R (n=2), V104L (n=2), G284R (n=2), G994D (n=1) |
| EGFR | FDA biomarker2004 · 7 drugs | curated target | amplification | 8 / 233 | 3.43% mutation 1.29% | — | 2 / 2 | 1.29–3.12% | V742I (n=1), V769_D770insG (n=1), N808D (n=1) |
| CTNNB1 | — | curated target | SNV / small indel | 15 / 233 | 6.44% | — | 1 / 2 | 0.0–6.44% | S45P (n=5), S37F (n=2), S45F (n=2), D32V (n=1), S33F (n=1) |
| SMAD4 | — | curated target | SNV / small indel | 51 / 233 | 21.89% | — | 2 / 2 | 3.12–21.89% | R361C (n=4), R361H (n=4), G386R (n=3), Q448* (n=2), D493G (n=2) |
| FGFR2 | FDA biomarker2019 · 4 drugs | curated target | SNV / small indel | 3 / 233 | 1.29% | — | 1 / 2 | 0.0–1.29% | F798L (n=1), G182E (n=1), T762Hfs*6 (n=1) |
| IDH1 | FDA biomarker2018 · 1 drug | curated target | SNV / small indel | 1 / 233 | 0.43% | — | 1 / 2 | 0.0–0.43% | M18I (n=1) |
| STK11 | — | by frequency | SNV / small indel | 22 / 233 | 9.44% | — | 1 / 2 | 0.0–9.44% | L117Ifs*45 (n=1), S216F (n=1), C134_V143del (n=1), G251R (n=1), F255Sfs*32 (n=1) |
| KMT2C | — | by frequency | SNV / small indel | 20 / 233 | 8.58% | — | 2 / 2 | 8.58–9.38% | Q2539* (n=1), P4655Sfs*5 (n=1), S2984Ffs*18 (n=1), Y4161Sfs*3 (n=1), R2307K (n=1) |
| ELF3 | — | by frequency | SNV / small indel | 20 / 186 | 10.75% | — | 2 / 2 | 6.25–10.75% | M324Nfs*147 (n=2), K304Qfs*167 (n=2), N83Kfs*9 (n=2), F92Mfs*2 (n=1), X334_splice (n=1) |
| ARID2 | — | by frequency | SNV / small indel | 20 / 233 | 8.58% | — | 2 / 2 | 6.25–8.58% | Q1016* (n=1), S319F (n=1), E12Wfs*38 (n=1), I37Nfs*29 (n=1), Q609* (n=1) |
| KMT2D | — | by frequency | SNV / small indel | 16 / 233 | 6.87% | — | 2 / 2 | 3.12–6.87% | G1235Vfs*95 (n=2), E1159Q (n=1), S2719N (n=1), P647Hfs*283 (n=1), P3131del (n=1) |
| ATM | FDA biomarker2020 · 1 drug | by frequency | SNV / small indel | 16 / 233 | 6.87% | — | 2 / 2 | 3.12–6.87% | R35Q (n=1), R2138Kfs*8 (n=1), D2725H (n=1), F2571Yfs*4 (n=1), I149del (n=1) |
| BRCA2 | FDA biomarker2014 · 1 drug | by frequency | SNV / small indel | 13 / 233 | 5.58% | — | 1 / 2 | 0.0–5.58% | R2520* (n=1), L1387F (n=1), I3171R (n=1), K1691Nfs*15 (n=1), E1641K (n=1) |
| RBM10 | — | by frequency | SNV / small indel | 11 / 233 | 4.72% | — | 1 / 2 | 0.0–4.72% | M731I (n=1), R21H (n=1), X68_splice (n=1), A421Rfs*19 (n=1), A553Hfs*73 (n=1) |
| RB1 | — | by frequency | SNV / small indel | 10 / 233 | 4.29% | — | 2 / 2 | 3.12–4.29% | Y655Lfs*13 (n=1), X406_splice (n=1), P2R (n=1), E817del (n=1), X737_splice (n=1) |
| PBRM1 | — | by frequency | SNV / small indel | 10 / 233 | 4.29% | — | 1 / 2 | 0.0–4.29% | E52* (n=1), S892_T895delinsKNI (n=1), I279Nfs*8 (n=1), R365C (n=1), N258Mfs*25 (n=1) |
| NF1 | FDA biomarker2020 · 1 drug | by frequency | SNV / small indel | 10 / 233 | 4.29% | — | 1 / 2 | 0.0–4.29% | X2274_splice (n=1), R304* (n=1), R416Q (n=1), X574_splice (n=1), H1494Qfs*7 (n=1) |
| KMT2A | — | by frequency | SNV / small indel | 10 / 233 | 4.29% | — | 1 / 2 | 0.0–4.29% | S2201F (n=1), P3522A (n=1), Q554Pfs*27 (n=1), K2658T (n=1), E2533* (n=1) |
| SLX4 | — | by frequency | SNV / small indel | 9 / 186 | 4.84% | — | 2 / 2 | 3.12–4.84% | T102Nfs*18 (n=1), R1468C (n=1), L1256V (n=1), S1134* (n=1), T162M (n=1) |
| PREX2 | — | by frequency | SNV / small indel | 9 / 186 | 4.84% | — | 2 / 2 | 3.12–4.84% | K60N (n=1), E550Q (n=1), Y758H (n=1), S1551C (n=1), F1318L (n=1) |
| KEAP1 | — | by frequency | SNV / small indel | 9 / 233 | 3.86% | — | 1 / 2 | 0.0–3.86% | R362Q (n=2), S102L (n=1), Y567* (n=1), L179R (n=1), D422N (n=1) |
| FBXW7 | — | by frequency | SNV / small indel | 9 / 233 | 3.86% | — | 2 / 2 | 3.12–3.86% | R479Q (n=2), R278* (n=1), S668Vfs*39 (n=1), R83K (n=1), L283Afs*3 (n=1) |
| AXIN1 | — | by frequency | SNV / small indel | 9 / 233 | 3.86% | — | 1 / 2 | 0.0–3.86% | E548* (n=1), E716* (n=1), W85* (n=1), E407* (n=1), Y148* (n=1) |
| ATRX | — | by frequency | SNV / small indel | 9 / 233 | 3.86% | — | 2 / 2 | 3.12–3.86% | S1996G (n=1), D1211E (n=1), Q2348* (n=1), R1803H (n=1), D699Gfs*2 (n=1) |
| RASA1 | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | R679* (n=1), R589H (n=1), A753T (n=1), R903* (n=1), S69L (n=1) |
| PTPRD | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | G203* (n=1), P516L (n=1), A395T (n=1), V330I (n=1), I476S (n=1) |
| NOTCH3 | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | A198G (n=1), R2207Q (n=1), T424A (n=1), G1105Afs*167 (n=1), A957T (n=1) |
| JAK1 | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | Q387Lfs*66 (n=1), V658Pfs*50 (n=1), Q986Rfs*29 (n=1), P733Gfs*3 (n=1), X663_splice (n=1) |
| IKZF1 | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | G151R (n=2), E387K (n=1), S445P (n=1), D399Efs*18 (n=1), S364W (n=1) |
| EP300 | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | K1569R (n=1), Q738H (n=1), P732del (n=1), Y1467C (n=1), T151A (n=1) |
| CDK12 | FDA biomarker2020 · 1 drug | by frequency | amplification | 16 / 233 | 6.87% mutation 3.43% | — | 1 / 2 | 0.0–3.43% | S102L (n=1), S176L (n=1), K132Sfs*5 (n=1), R981C (n=1), E189K (n=1) |
| ARID1B | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | X1115_splice (n=1), R1075* (n=1), Q905Hfs*6 (n=1), S736Ifs*27 (n=1), P735Hfs*10 (n=1) |
| APC | — | by frequency | SNV / small indel | 8 / 233 | 3.43% | — | 1 / 2 | 0.0–3.43% | Q358* (n=1), Q1541* (n=1), I1574V (n=1), G1499* (n=1), *2844Eext*27 (n=1) |
| ZFHX3 | — | by frequency | SNV / small indel | 7 / 225 | 3.11% | — | 1 / 2 | 0.0–3.11% | X1177_splice (n=2), S1658T (n=1), A3407Lfs*78 (n=1), G3521S (n=1), P3218A (n=1) |
| RNF43 | — | by frequency | SNV / small indel | 7 / 233 | 3.0% | — | 1 / 2 | 0.0–3.0% | G659Vfs*41 (n=3), R371* (n=2), P369T (n=1), I186F (n=1), S121* (n=1) |
| PTPRS | — | by frequency | SNV / small indel | 7 / 233 | 3.0% | — | 2 / 2 | 3.0–3.12% | R148Q (n=2), Q1009H (n=1), R1696C (n=1), P1809L (n=1), E1928K (n=1) |
| PTEN | — | by frequency | SNV / small indel | 7 / 233 | 3.0% | — | 1 / 2 | 0.0–3.0% | R130Q (n=1), D19Gfs*25 (n=1), Q245* (n=1), K267Rfs*9 (n=1), R130* (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 |
|---|---|---|---|---|---|---|---|---|---|
| Gallbladder Cancer (MSK, 2022) reference | gbc_mskcc_2022 | 233 observed | 244 / 244 | targeted panel | IMPACT468 (151), IMPACT410 (44), IMPACT505 (40), IMPACT341 (9) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 5.0 |
| Gallbladder Carcinoma (Shanghai, Nat Genet 2014) | gbc_shanghai_2014 | 32 observed | 32 / 32 | exome or genome | WES (32) | hg19 | SNV, small indel | 0 | 29.0 |
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 | 35 | 233 | 15.02% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| ERBB2 | amplification | 24 | 233 | 10.3% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| CDK12 | amplification | 16 | 233 | 6.87% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| ERBB3 | amplification | 12 | 233 | 5.15% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| SMAD4 | deep deletion | 11 | 233 | 4.72% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| KRAS | amplification | 10 | 233 | 4.29% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| EGFR | amplification | 8 | 233 | 3.43% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| RB1 | deep deletion | 7 | 233 | 3.0% | gbc_mskcc_2022 | gbc_mskcc_2022_cna |
| ARID1B | deep deletion | 5 | 233 | 2.15% | gbc_mskcc_2022 | gbc_mskcc_2022_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) |
|---|---|---|
| ERBB2 | 7.3–9.38% | gbc_mskcc_2022: 17/233 (7.3%) · gbc_shanghai_2014: 3/32 (9.38%) |
| TP53 | 25.0–63.95% | gbc_mskcc_2022: 149/233 (63.95%) · gbc_shanghai_2014: 8/32 (25.0%) |
| KRAS | 0.0–7.73% | gbc_mskcc_2022: 18/233 (7.73%) · gbc_shanghai_2014: 0/32 (0.0%) |
| PIK3CA | 6.25–10.73% | gbc_mskcc_2022: 25/233 (10.73%) · gbc_shanghai_2014: 2/32 (6.25%) |
| CDKN2A | 0.0–9.87% | gbc_mskcc_2022: 23/233 (9.87%) · gbc_shanghai_2014: 0/32 (0.0%) |
| ARID1A | 6.25–20.6% | gbc_mskcc_2022: 48/233 (20.6%) · gbc_shanghai_2014: 2/32 (6.25%) |
| ERBB3 | 6.44–9.38% | gbc_mskcc_2022: 15/233 (6.44%) · gbc_shanghai_2014: 3/32 (9.38%) |
| EGFR | 1.29–3.12% | gbc_mskcc_2022: 3/233 (1.29%) · gbc_shanghai_2014: 1/32 (3.12%) |
| CTNNB1 | 0.0–6.44% | gbc_mskcc_2022: 15/233 (6.44%) · gbc_shanghai_2014: 0/32 (0.0%) |
| SMAD4 | 3.12–21.89% | gbc_mskcc_2022: 51/233 (21.89%) · gbc_shanghai_2014: 1/32 (3.12%) |
| FGFR2 | 0.0–1.29% | gbc_mskcc_2022: 3/233 (1.29%) · gbc_shanghai_2014: 0/32 (0.0%) |
| IDH1 | 0.0–0.43% | gbc_mskcc_2022: 1/233 (0.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| STK11 | 0.0–9.44% | gbc_mskcc_2022: 22/233 (9.44%) · gbc_shanghai_2014: 0/32 (0.0%) |
| KMT2C | 8.58–9.38% | gbc_mskcc_2022: 20/233 (8.58%) · gbc_shanghai_2014: 3/32 (9.38%) |
| ELF3 | 6.25–10.75% | gbc_mskcc_2022: 20/186 (10.75%) · gbc_shanghai_2014: 2/32 (6.25%) |
| ARID2 | 6.25–8.58% | gbc_mskcc_2022: 20/233 (8.58%) · gbc_shanghai_2014: 2/32 (6.25%) |
| KMT2D | 3.12–6.87% | gbc_mskcc_2022: 16/233 (6.87%) · gbc_shanghai_2014: 1/32 (3.12%) |
| ATM | 3.12–6.87% | gbc_mskcc_2022: 16/233 (6.87%) · gbc_shanghai_2014: 1/32 (3.12%) |
| BRCA2 | 0.0–5.58% | gbc_mskcc_2022: 13/233 (5.58%) · gbc_shanghai_2014: 0/32 (0.0%) |
| RBM10 | 0.0–4.72% | gbc_mskcc_2022: 11/233 (4.72%) · gbc_shanghai_2014: 0/32 (0.0%) |
| RB1 | 3.12–4.29% | gbc_mskcc_2022: 10/233 (4.29%) · gbc_shanghai_2014: 1/32 (3.12%) |
| PBRM1 | 0.0–4.29% | gbc_mskcc_2022: 10/233 (4.29%) · gbc_shanghai_2014: 0/32 (0.0%) |
| NF1 | 0.0–4.29% | gbc_mskcc_2022: 10/233 (4.29%) · gbc_shanghai_2014: 0/32 (0.0%) |
| KMT2A | 0.0–4.29% | gbc_mskcc_2022: 10/233 (4.29%) · gbc_shanghai_2014: 0/32 (0.0%) |
| SLX4 | 3.12–4.84% | gbc_mskcc_2022: 9/186 (4.84%) · gbc_shanghai_2014: 1/32 (3.12%) |
| PREX2 | 3.12–4.84% | gbc_mskcc_2022: 9/186 (4.84%) · gbc_shanghai_2014: 1/32 (3.12%) |
| KEAP1 | 0.0–3.86% | gbc_mskcc_2022: 9/233 (3.86%) · gbc_shanghai_2014: 0/32 (0.0%) |
| FBXW7 | 3.12–3.86% | gbc_mskcc_2022: 9/233 (3.86%) · gbc_shanghai_2014: 1/32 (3.12%) |
| AXIN1 | 0.0–3.86% | gbc_mskcc_2022: 9/233 (3.86%) · gbc_shanghai_2014: 0/32 (0.0%) |
| ATRX | 3.12–3.86% | gbc_mskcc_2022: 9/233 (3.86%) · gbc_shanghai_2014: 1/32 (3.12%) |
| RASA1 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| PTPRD | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| NOTCH3 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| JAK1 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| IKZF1 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| EP300 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| CDK12 | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| ARID1B | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| APC | 0.0–3.43% | gbc_mskcc_2022: 8/233 (3.43%) · gbc_shanghai_2014: 0/32 (0.0%) |
| ZFHX3 | 0.0–3.11% | gbc_mskcc_2022: 7/225 (3.11%) · gbc_shanghai_2014: 0/32 (0.0%) |
| RNF43 | 0.0–3.0% | gbc_mskcc_2022: 7/233 (3.0%) · gbc_shanghai_2014: 0/32 (0.0%) |
| PTPRS | 3.0–3.12% | gbc_mskcc_2022: 7/233 (3.0%) · gbc_shanghai_2014: 1/32 (3.12%) |
| PTEN | 0.0–3.0% | gbc_mskcc_2022: 7/233 (3.0%) · gbc_shanghai_2014: 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 2026-09-18; 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.
- 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/gallbladder-cancer.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.