Disease intelligence · mutation landscape
Hepatocellular carcinoma mutation landscape
How often each gene is altered in hepatocellular 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 Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas) (366 sequenced patients, exome or genome), the most frequently altered of the 47 genes shown are TP53 29.51%, CTNNB1 25.96%, ALB 12.84%, CACNA1E 7.9% (amplification), ARID1A 7.65%. Each figure divides by the patients on whom that gene could be called.
2 of 366 patients are hypermutated (more than 790 non-silent mutations, ten times the cohort median of 79); every gene's frequency without them is beside the headline.
Of the briefing's 11 curated targets, 3 are altered in under 2% of this cohort (FGFR4, KDR, GPC3): 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 | lihc_tcga_pan_can_atlas_2018 366 pts · exome or genome | hcc_inserm_fr_2015 243 pts · exome or genome | hcc_msk_2024 1370 pts · targeted panel |
|---|---|---|---|
| TERT SNV / small indel | 0.55%2/366 | 57.2%139/243 | 16.42%225/1370 |
| TERT promoter | · | 56.79%138/243 | 16.13%221/1370 |
| TERT amplification | 5.45%20/367 | · | 1.75%24/1370 |
| TP53 SNV / small indel | 29.51%108/366 | 22.22%54/243 | 34.01%466/1370 |
| TP53 deep deletion | 2.45%9/367 | · | 0.66%9/1370 |
| CTNNB1 SNV / small indel | 25.96%95/366 | 36.21%88/243 | 9.64%132/1370 |
| AXIN1 SNV / small indel | 6.83%25/366 | 8.64%21/243 | 2.85%39/1370 |
| ARID1A SNV / small indel | 7.65%28/366 | 9.88%24/243 | 16.5%226/1370 |
| MET SNV / small indel | 0.55%2/366 | 0.41%1/243 | 0.73%10/1370 |
| MET amplification | 2.45%9/367 | · | 1.31%18/1370 |
| FGF19 SNV / small indel | 0% | 0.41%1/243 | 0.15%2/1370 |
| FGF19 amplification | 6.81%25/367 | · | 4.38%60/1370 |
| FGFR4 SNV / small indel | 1.09%4/366 | 0.41%1/243 | 0.36%5/1370 |
| KDR SNV / small indel | 1.91%7/366 | 0.82%2/243 | 1.31%18/1370 |
| VEGFA SNV / small indel | 0% | 0% | 0.23%3/1284 |
| VEGFA amplification | 6.54%24/367 | · | 1.61%22/1370 |
| GPC3 SNV / small indel | 0.55%2/366 | 0.41%1/243 | · |
| ALB SNV / small indel | 12.84%47/366 | 10.7%26/243 | 8.14%18/221 |
| CACNA1E SNV / small indel | 7.65%28/366 | 2.47%6/243 | · |
| CACNA1E amplification | 7.9%29/367 | · | 0% |
| PRKDC SNV / small indel | 6.01%22/366 | 2.06%5/243 | · |
| PRKDC amplification | 5.45%20/367 | · | 0% |
| DOCK2 SNV / small indel | 6.01%22/366 | 3.7%9/243 | · |
| WDR87 SNV / small indel | 5.46%20/366 | 2.47%6/243 | · |
| SDK1 SNV / small indel | 5.46%20/366 | 3.29%8/243 | · |
| HERC2 SNV / small indel | 5.46%20/366 | 2.88%7/243 | · |
| FRAS1 SNV / small indel | 5.46%20/366 | 5.35%13/243 | · |
| BAP1 SNV / small indel | 5.46%20/366 | 1.65%4/243 | 8.54%117/1370 |
| RB1 SNV / small indel | 5.19%19/366 | 3.29%8/243 | 3.21%44/1370 |
| RB1 deep deletion | 5.18%19/367 | · | 1.24%17/1370 |
| PCDH15 SNV / small indel | 5.19%19/366 | 6.17%15/243 | · |
| LRP1 SNV / small indel | 5.19%19/366 | 2.47%6/243 | · |
| KMT2D SNV / small indel | 5.19%19/366 | 5.76%14/243 | 4.67%64/1370 |
| FREM2 SNV / small indel | 5.19%19/366 | 2.88%7/243 | · |
| FASN SNV / small indel | 5.19%19/366 | 3.7%9/243 | · |
| FASN amplification | 4.9%18/367 | · | 0% |
| BIRC6 SNV / small indel | 5.19%19/366 | 3.7%9/243 | · |
| ARID2 SNV / small indel | 5.19%19/366 | 6.17%15/243 | 4.89%67/1370 |
| UNC80 SNV / small indel | 4.92%18/366 | 3.29%8/243 | · |
| PRUNE2 SNV / small indel | 4.92%18/366 | 3.7%9/243 | · |
| PREX2 SNV / small indel | 4.92%18/366 | 4.94%12/243 | 3.51%35/998 |
| PREX2 amplification | 6.54%24/367 | · | 1.02%14/1370 |
| NBEA SNV / small indel | 4.92%18/366 | 3.7%9/243 | · |
| LAMA1 SNV / small indel | 4.92%18/366 | 3.29%8/243 | · |
| KEAP1 SNV / small indel | 4.92%18/366 | 3.7%9/243 | 1.9%26/1370 |
| HTT SNV / small indel | 4.92%18/366 | 0.82%2/243 | · |
| EYS SNV / small indel | 4.92%18/366 | 2.06%5/243 | · |
| EYS amplification | 3.81%14/367 | · | 0% |
| DCHS1 SNV / small indel | 4.92%18/366 | 2.88%7/243 | · |
| COL6A6 SNV / small indel | 4.92%18/366 | 1.23%3/243 | · |
| ABCA12 SNV / small indel | 4.92%18/366 | 1.23%3/243 | · |
| PTPRQ SNV / small indel | 4.64%17/366 | 2.88%7/243 | · |
| PKHD1 SNV / small indel | 4.64%17/366 | 3.7%9/243 | · |
| PKHD1 amplification | 2.18%8/367 | · | 0% |
| MYT1L SNV / small indel | 4.64%17/366 | 1.23%3/243 | · |
| KMT2C SNV / small indel | 4.64%17/366 | 2.47%6/243 | 5.04%69/1370 |
| FAT2 SNV / small indel | 4.64%17/366 | 2.88%7/243 | · |
| LRRIQ1 SNV / small indel | 4.37%16/366 | 2.88%7/243 | · |
| FMN2 SNV / small indel | 4.37%16/366 | 1.65%4/243 | · |
| FMN2 amplification | 6.27%23/367 | · | 0% |
| FCGBP SNV / small indel | 4.37%16/366 | 3.29%8/243 | · |
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 108 of 366 patients in Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas).
CTNNB1 is mutated in 95 of 366 patients in Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas).
ALB is mutated in 47 of 366 patients in Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
TERT: The headline is coding change only: Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas) reports no promoter calls, and whole-exome sequencing does not cover the TERT promoter. Where it is assayed the figure is 138/243 (56.79%) in Hepatocellular Carcinomas (INSERM, Nat Genet 2015). The two are not pooled and the headline is not adjusted.
Headline values are from the reference cohort, lihc_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 |
|---|---|---|---|---|---|---|---|---|---|
| TERT | — | curated target | amplification | 20 / 367 | 5.45% mutation 0.55%coding only | 0.55% | 3 / 3 | 0.55–57.2% | V741L (n=1), K236T (n=1) |
| TP53 | — | curated target | SNV / small indel | 108 / 366 | 29.51% | 29.12% | 3 / 3 | 22.22–34.01% | R249S (n=11), H193R (n=4), X126_splice (n=3), V157F (n=3), R248Q (n=3) |
| CTNNB1 | — | curated target | SNV / small indel | 95 / 366 | 25.96% | 25.82% | 3 / 3 | 9.64–36.21% | S45P (n=11), D32G (n=7), K335I (n=6), S33C (n=6), T41A (n=5) |
| AXIN1 | — | curated target | SNV / small indel | 25 / 366 | 6.83% | 6.87% | 3 / 3 | 2.85–8.64% | X340_splice (n=2), X293_splice (n=1), S225Pfs*17 (n=1), L471Pfs*120 (n=1), W635* (n=1) |
| ARID1A | — | curated target | SNV / small indel | 28 / 366 | 7.65% | 7.69% | 3 / 3 | 7.65–16.5% | P728Qfs*87 (n=2), Q1142* (n=2), A1687Dfs*2 (n=1), Q1974Tfs*43 (n=1), A2234Gfs*34 (n=1) |
| MET | FDA biomarker2020 · 2 drugs | curated target | amplification | 9 / 367 | 2.45% mutation 0.55% | 0.55% | 3 / 3 | 0.41–0.73% | H1238L (n=1), S22I (n=1) |
| FGF19 | — | curated target | amplification | 25 / 367 | 6.81% mutation 0.0% | 0.0% | 2 / 3 | 0.0–0.41% | none recurrent |
| FGFR4 | — | curated target | SNV / small indel | 4 / 366 | 1.09% | 0.82% | 3 / 3 | 0.36–1.09% | R437C (n=1), L467M (n=1), S377F (n=1), R196H (n=1) |
| KDR | — | curated target | SNV / small indel | 7 / 366 | 1.91% | 1.65% | 3 / 3 | 0.82–1.91% | D433Y (n=1), Y1319* (n=1), G800R (n=1), I456M (n=1), A352S (n=1) |
| VEGFA | — | curated target | amplification | 24 / 367 | 6.54% mutation 0.0% | 0.0% | 1 / 3 | 0.0–0.23% | none recurrent |
| GPC3 | — | curated target | deep deletion | 7 / 367 | 1.91% mutation 0.55% | 0.55% | 2 / 3 | 0.41–0.55% | K347N (n=1), K206N (n=1) |
| ALB | — | by frequency | SNV / small indel | 47 / 366 | 12.84% | 12.91% | 3 / 3 | 8.14–12.84% | X161_splice (n=5), X476_splice (n=3), V448Cfs*16 (n=2), R221Tfs*30 (n=2), A374S (n=1) |
| CACNA1E | — | by frequency | amplification | 29 / 367 | 7.9% mutation 7.65% | 7.14% | 2 / 3 | 2.47–7.65% | N255I (n=2), N1357S (n=1), V1409A (n=1), R378H (n=1), P2144L (n=1) |
| PRKDC | — | by frequency | SNV / small indel | 22 / 366 | 6.01% | 5.77% | 2 / 3 | 2.06–6.01% | X270_splice (n=2), W601C (n=1), R2728L (n=1), K1074* (n=1), D3756V (n=1) |
| DOCK2 | — | by frequency | SNV / small indel | 22 / 366 | 6.01% | 5.49% | 2 / 3 | 3.7–6.01% | Y1555* (n=1), Y257H (n=1), Q996* (n=1), R1446W (n=1), Q878K (n=1) |
| WDR87 | — | by frequency | SNV / small indel | 20 / 366 | 5.46% | 5.22% | 2 / 3 | 2.47–5.46% | E1898* (n=2), Q1897H (n=2), I2076M (n=1), R2437Sfs*6 (n=1), P2389H (n=1) |
| SDK1 | — | by frequency | SNV / small indel | 20 / 366 | 5.46% | 5.49% | 2 / 3 | 3.29–5.46% | G653A (n=1), L568F (n=1), L1483H (n=1), A847G (n=1), R168H (n=1) |
| HERC2 | — | by frequency | SNV / small indel | 20 / 366 | 5.46% | 5.49% | 2 / 3 | 2.88–5.46% | G2804C (n=1), E3307K (n=1), A4155V (n=1), K2304* (n=1), S2548R (n=1) |
| FRAS1 | — | by frequency | SNV / small indel | 20 / 366 | 5.46% | 5.22% | 2 / 3 | 5.35–5.46% | Q1411* (n=1), P3679L (n=1), E393G (n=1), X2344_splice (n=1), S3118F (n=1) |
| BAP1 | — | by frequency | SNV / small indel | 20 / 366 | 5.46% | 5.49% | 3 / 3 | 1.65–8.54% | W202L (n=1), A359Tfs*68 (n=1), X662_splice (n=1), M115Rfs*9 (n=1), P235_R237del (n=1) |
| RB1 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 4.95% | 3 / 3 | 3.21–5.19% | N399Kfs*7 (n=2), N290Kfs*20 (n=1), V759_L769del (n=1), I66K (n=1), P67A (n=1) |
| PCDH15 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 5.22% | 2 / 3 | 5.19–6.17% | R1514Q (n=1), G655* (n=1), Q401E (n=1), E294* (n=1), R683C (n=1) |
| LRP1 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 4.95% | 2 / 3 | 2.47–5.19% | G1431C (n=2), T4331S (n=1), A1009D (n=1), T778Lfs*2 (n=1), S1997F (n=1) |
| KMT2D | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 4.67% | 3 / 3 | 4.67–5.76% | E541K (n=1), R3547H (n=1), S3Tfs*4 (n=1), D3039G (n=1), E4418Nfs*14 (n=1) |
| FREM2 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 4.95% | 2 / 3 | 2.88–5.19% | D1333H (n=2), E1192* (n=2), G5R (n=1), P1903L (n=1), E1610Q (n=1) |
| FASN | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 5.22% | 2 / 3 | 3.7–5.19% | F146S (n=2), I1057V (n=1), E1136D (n=1), G102E (n=1), E660* (n=1) |
| BIRC6 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 4.67% | 2 / 3 | 3.7–5.19% | F4598V (n=1), V2162A (n=1), R3939K (n=1), I242* (n=1), E550* (n=1) |
| ARID2 | — | by frequency | SNV / small indel | 19 / 366 | 5.19% | 5.22% | 3 / 3 | 4.89–6.17% | L370* (n=1), P1487Qfs*25 (n=1), X1592_splice (n=1), N309Y (n=1), C1667* (n=1) |
| UNC80 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 3.29–4.92% | G1551R (n=1), L1568S (n=1), S630I (n=1), S2414R (n=1), H1014L (n=1) |
| PRUNE2 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 3.7–4.92% | P3045Qfs*11 (n=1), W919R (n=1), S576I (n=1), G1492V (n=1), Y1088S (n=1) |
| PREX2 | — | by frequency | amplification | 24 / 367 | 6.54% mutation 4.92% | 4.67% | 3 / 3 | 3.51–4.94% | L1162I (n=1), R363Q (n=1), I925N (n=1), A1467S (n=1), E121Q (n=1) |
| NBEA | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 3.7–4.92% | D2673Rfs*17 (n=2), R1580H (n=2), Y917C (n=2), N1950Y (n=1), F403C (n=1) |
| LAMA1 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.95% | 2 / 3 | 3.29–4.92% | Y2845H (n=1), S2615N (n=1), A880D (n=1), A989D (n=1), X2392_splice (n=1) |
| KEAP1 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.95% | 3 / 3 | 1.9–4.92% | L355Sfs*37 (n=1), V152G (n=1), S592G (n=1), G186S (n=1), P278L (n=1) |
| HTT | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 0.82–4.92% | Q3085H (n=1), T3026A (n=1), G3081A (n=1), W2623L (n=1), Q2030Afs*43 (n=1) |
| EYS | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 2.06–4.92% | A1497D (n=1), N2484D (n=1), I1328F (n=1), R1252I (n=1), Q677* (n=1) |
| DCHS1 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 2.88–4.92% | C3193F (n=2), R112W (n=1), A3262P (n=1), R719L (n=1), P2857H (n=1) |
| COL6A6 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.67% | 2 / 3 | 1.23–4.92% | K617R (n=2), V663L (n=1), C539R (n=1), A1861E (n=1), M959R (n=1) |
| ABCA12 | — | by frequency | SNV / small indel | 18 / 366 | 4.92% | 4.4% | 2 / 3 | 1.23–4.92% | G1614E (n=2), T1842S (n=1), P1288L (n=1), S1064I (n=1), S230T (n=1) |
| PTPRQ | — | by frequency | SNV / small indel | 17 / 366 | 4.64% | 4.4% | 2 / 3 | 2.88–4.64% | E1621Q (n=2), V1701I (n=1), I1839N (n=1), D1253Y (n=1), S490R (n=1) |
| PKHD1 | — | by frequency | SNV / small indel | 17 / 366 | 4.64% | 4.4% | 2 / 3 | 3.7–4.64% | P1258R (n=1), I3909M (n=1), I2539T (n=1), V595F (n=1), N977D (n=1) |
| MYT1L | — | by frequency | SNV / small indel | 17 / 366 | 4.64% | 4.67% | 2 / 3 | 1.23–4.64% | R358C (n=1), N1134S (n=1), G1045R (n=1), E27* (n=1), D119E (n=1) |
| KMT2C | — | by frequency | SNV / small indel | 17 / 366 | 4.64% | 4.67% | 3 / 3 | 2.47–5.04% | V9M (n=1), *4912Lext*36 (n=1), E1623* (n=1), H367D (n=1), C310F (n=1) |
| FAT2 | — | by frequency | SNV / small indel | 17 / 366 | 4.64% | 4.4% | 2 / 3 | 2.88–4.64% | D882G (n=1), I138S (n=1), R1006S (n=1), L1514F (n=1), X1316_splice (n=1) |
| LRRIQ1 | — | by frequency | SNV / small indel | 16 / 366 | 4.37% | 4.4% | 2 / 3 | 2.88–4.37% | R491Tfs*14 (n=1), I1474F (n=1), K1335E (n=1), S618L (n=1), S1466* (n=1) |
| FMN2 | — | by frequency | amplification | 23 / 367 | 6.27% mutation 4.37% | 4.4% | 2 / 3 | 1.65–4.37% | P909S (n=1), A357V (n=1), A526V (n=1), X663_splice (n=1), I1074L (n=1) |
| FCGBP | — | by frequency | SNV / small indel | 16 / 366 | 4.37% | 4.4% | 2 / 3 | 3.29–4.37% | R5150H (n=1), C3889F (n=1), G312V (n=1), G805C (n=1), L3740M (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 |
|---|---|---|---|---|---|---|---|---|---|
| Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas) reference | lihc_tcga_pan_can_atlas_2018 | 366 observed | 366 / 372 | exome or genome | WES (366) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 2 | 79.0 |
| Hepatocellular Carcinomas (INSERM, Nat Genet 2015) | hcc_inserm_fr_2015 | 243 observed | 243 / 243 | exome or genome | WES (243) | hg19 | SNV, small indel | 1 | 61 |
| Hepatocellular Carcinoma (MSK, Clin Cancer Res 2024) | hcc_msk_2024 | 1370 observed | 1370 / 1370 | targeted panel | IMPACT468 (777), IMPACT410 (286), IMPACT505 (221), IMPACT341 (86) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 3.0 |
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 |
|---|---|---|---|---|---|---|
| CACNA1E | amplification | 29 | 367 | 7.9% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| FGF19 | amplification | 25 | 367 | 6.81% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| VEGFA | amplification | 24 | 367 | 6.54% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| PREX2 | amplification | 24 | 367 | 6.54% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| FMN2 | amplification | 23 | 367 | 6.27% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| TERT | amplification | 20 | 367 | 5.45% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| PRKDC | amplification | 20 | 367 | 5.45% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 19 | 367 | 5.18% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| FASN | amplification | 18 | 367 | 4.9% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| FGF19 | amplification | 60 | 1370 | 4.38% | hcc_msk_2024 | hcc_msk_2024_cna |
| EYS | amplification | 14 | 367 | 3.81% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| TP53 | deep deletion | 9 | 367 | 2.45% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| MET | amplification | 9 | 367 | 2.45% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_gistic |
| PKHD1 | amplification | 8 | 367 | 2.18% | lihc_tcga_pan_can_atlas_2018 | lihc_tcga_pan_can_atlas_2018_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) |
|---|---|---|
| TERT | 0.55–57.2% | lihc_tcga_pan_can_atlas_2018: 2/366 (0.55%) · hcc_inserm_fr_2015: 139/243 (57.2%) · hcc_msk_2024: 225/1370 (16.42%) |
| TP53 | 22.22–34.01% | lihc_tcga_pan_can_atlas_2018: 108/366 (29.51%) · hcc_inserm_fr_2015: 54/243 (22.22%) · hcc_msk_2024: 466/1370 (34.01%) |
| CTNNB1 | 9.64–36.21% | lihc_tcga_pan_can_atlas_2018: 95/366 (25.96%) · hcc_inserm_fr_2015: 88/243 (36.21%) · hcc_msk_2024: 132/1370 (9.64%) |
| AXIN1 | 2.85–8.64% | lihc_tcga_pan_can_atlas_2018: 25/366 (6.83%) · hcc_inserm_fr_2015: 21/243 (8.64%) · hcc_msk_2024: 39/1370 (2.85%) |
| ARID1A | 7.65–16.5% | lihc_tcga_pan_can_atlas_2018: 28/366 (7.65%) · hcc_inserm_fr_2015: 24/243 (9.88%) · hcc_msk_2024: 226/1370 (16.5%) |
| MET | 0.41–0.73% | lihc_tcga_pan_can_atlas_2018: 2/366 (0.55%) · hcc_inserm_fr_2015: 1/243 (0.41%) · hcc_msk_2024: 10/1370 (0.73%) |
| FGF19 | 0.0–0.41% | lihc_tcga_pan_can_atlas_2018: 0/366 (0.0%) · hcc_inserm_fr_2015: 1/243 (0.41%) · hcc_msk_2024: 2/1370 (0.15%) |
| FGFR4 | 0.36–1.09% | lihc_tcga_pan_can_atlas_2018: 4/366 (1.09%) · hcc_inserm_fr_2015: 1/243 (0.41%) · hcc_msk_2024: 5/1370 (0.36%) |
| KDR | 0.82–1.91% | lihc_tcga_pan_can_atlas_2018: 7/366 (1.91%) · hcc_inserm_fr_2015: 2/243 (0.82%) · hcc_msk_2024: 18/1370 (1.31%) |
| VEGFA | 0.0–0.23% | lihc_tcga_pan_can_atlas_2018: 0/366 (0.0%) · hcc_inserm_fr_2015: 0/243 (0.0%) · hcc_msk_2024: 3/1284 (0.23%) |
| GPC3 | 0.41–0.55% | lihc_tcga_pan_can_atlas_2018: 2/366 (0.55%) · hcc_inserm_fr_2015: 1/243 (0.41%) · hcc_msk_2024: not assayed |
| ALB | 8.14–12.84% | lihc_tcga_pan_can_atlas_2018: 47/366 (12.84%) · hcc_inserm_fr_2015: 26/243 (10.7%) · hcc_msk_2024: 18/221 (8.14%) |
| CACNA1E | 2.47–7.65% | lihc_tcga_pan_can_atlas_2018: 28/366 (7.65%) · hcc_inserm_fr_2015: 6/243 (2.47%) · hcc_msk_2024: not assayed |
| PRKDC | 2.06–6.01% | lihc_tcga_pan_can_atlas_2018: 22/366 (6.01%) · hcc_inserm_fr_2015: 5/243 (2.06%) · hcc_msk_2024: not assayed |
| DOCK2 | 3.7–6.01% | lihc_tcga_pan_can_atlas_2018: 22/366 (6.01%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| WDR87 | 2.47–5.46% | lihc_tcga_pan_can_atlas_2018: 20/366 (5.46%) · hcc_inserm_fr_2015: 6/243 (2.47%) · hcc_msk_2024: not assayed |
| SDK1 | 3.29–5.46% | lihc_tcga_pan_can_atlas_2018: 20/366 (5.46%) · hcc_inserm_fr_2015: 8/243 (3.29%) · hcc_msk_2024: not assayed |
| HERC2 | 2.88–5.46% | lihc_tcga_pan_can_atlas_2018: 20/366 (5.46%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| FRAS1 | 5.35–5.46% | lihc_tcga_pan_can_atlas_2018: 20/366 (5.46%) · hcc_inserm_fr_2015: 13/243 (5.35%) · hcc_msk_2024: not assayed |
| BAP1 | 1.65–8.54% | lihc_tcga_pan_can_atlas_2018: 20/366 (5.46%) · hcc_inserm_fr_2015: 4/243 (1.65%) · hcc_msk_2024: 117/1370 (8.54%) |
| RB1 | 3.21–5.19% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 8/243 (3.29%) · hcc_msk_2024: 44/1370 (3.21%) |
| PCDH15 | 5.19–6.17% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 15/243 (6.17%) · hcc_msk_2024: not assayed |
| LRP1 | 2.47–5.19% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 6/243 (2.47%) · hcc_msk_2024: not assayed |
| KMT2D | 4.67–5.76% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 14/243 (5.76%) · hcc_msk_2024: 64/1370 (4.67%) |
| FREM2 | 2.88–5.19% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| FASN | 3.7–5.19% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| BIRC6 | 3.7–5.19% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| ARID2 | 4.89–6.17% | lihc_tcga_pan_can_atlas_2018: 19/366 (5.19%) · hcc_inserm_fr_2015: 15/243 (6.17%) · hcc_msk_2024: 67/1370 (4.89%) |
| UNC80 | 3.29–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 8/243 (3.29%) · hcc_msk_2024: not assayed |
| PRUNE2 | 3.7–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| PREX2 | 3.51–4.94% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 12/243 (4.94%) · hcc_msk_2024: 35/998 (3.51%) |
| NBEA | 3.7–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| LAMA1 | 3.29–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 8/243 (3.29%) · hcc_msk_2024: not assayed |
| KEAP1 | 1.9–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: 26/1370 (1.9%) |
| HTT | 0.82–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 2/243 (0.82%) · hcc_msk_2024: not assayed |
| EYS | 2.06–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 5/243 (2.06%) · hcc_msk_2024: not assayed |
| DCHS1 | 2.88–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| COL6A6 | 1.23–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 3/243 (1.23%) · hcc_msk_2024: not assayed |
| ABCA12 | 1.23–4.92% | lihc_tcga_pan_can_atlas_2018: 18/366 (4.92%) · hcc_inserm_fr_2015: 3/243 (1.23%) · hcc_msk_2024: not assayed |
| PTPRQ | 2.88–4.64% | lihc_tcga_pan_can_atlas_2018: 17/366 (4.64%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| PKHD1 | 3.7–4.64% | lihc_tcga_pan_can_atlas_2018: 17/366 (4.64%) · hcc_inserm_fr_2015: 9/243 (3.7%) · hcc_msk_2024: not assayed |
| MYT1L | 1.23–4.64% | lihc_tcga_pan_can_atlas_2018: 17/366 (4.64%) · hcc_inserm_fr_2015: 3/243 (1.23%) · hcc_msk_2024: not assayed |
| KMT2C | 2.47–5.04% | lihc_tcga_pan_can_atlas_2018: 17/366 (4.64%) · hcc_inserm_fr_2015: 6/243 (2.47%) · hcc_msk_2024: 69/1370 (5.04%) |
| FAT2 | 2.88–4.64% | lihc_tcga_pan_can_atlas_2018: 17/366 (4.64%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| LRRIQ1 | 2.88–4.37% | lihc_tcga_pan_can_atlas_2018: 16/366 (4.37%) · hcc_inserm_fr_2015: 7/243 (2.88%) · hcc_msk_2024: not assayed |
| FMN2 | 1.65–4.37% | lihc_tcga_pan_can_atlas_2018: 16/366 (4.37%) · hcc_inserm_fr_2015: 4/243 (1.65%) · hcc_msk_2024: not assayed |
| FCGBP | 3.29–4.37% | lihc_tcga_pan_can_atlas_2018: 16/366 (4.37%) · hcc_inserm_fr_2015: 8/243 (3.29%) · hcc_msk_2024: not assayed |
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/hepatocellular-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.