Disease intelligence · mutation landscape
Prostate cancer mutation landscape
How often each gene is altered in prostate 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 Prostate Adenocarcinoma (TCGA, PanCancer Atlas) (494 sequenced patients, exome or genome), the most frequently altered of the 48 genes shown are PTEN 17.38% (deep deletion), TMPRSS2 11.86% (deep deletion), TP53 11.54%, SPOP 11.13%, ERG 10.02% (deep deletion). Each figure divides by the patients on whom that gene could be called.
4 of 494 patients are hypermutated (more than 260 non-silent mutations, ten times the cohort median of 26); every gene's frequency without them is beside the headline.
Of the briefing's 12 curated targets, 4 are altered in under 2% of this cohort (AR, FOLH1, CYP17A1, KLK3): 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 | prad_tcga_pan_can_atlas_2018 494 pts · exome or genome | prad_p1000 1013 pts · exome or genome | prostate_msk_2024 2257 pts · targeted panel |
|---|---|---|---|
| AR SNV / small indel | 0.4%2/494 | 4.74%48/1013 | 4.12%93/2257 |
| AR amplification | 1.02%5/489 | 12.54%127/1013 | 10.46%236/2257 |
| FOLH1 SNV / small indel | 0% | 0.1%1/1013 | · |
| FOLH1 deep deletion | 0.41%2/489 | 2.17%22/1013 | 0% |
| CYP17A1 SNV / small indel | 0.2%1/494 | 0.2%2/1013 | · |
| BRCA2 SNV / small indel | 1.62%8/494 | 2.86%29/1013 | 3.99%90/2257 |
| BRCA2 deep deletion | 3.48%17/489 | 2.47%25/1013 | 2.17%49/2257 |
| ATM SNV / small indel | 4.05%20/494 | 3.75%38/1013 | 4.25%96/2257 |
| PTEN SNV / small indel | 3.64%18/494 | 4.24%43/1013 | 7.98%180/2257 |
| PTEN deep deletion | 17.38%85/489 | 12.24%124/1013 | 11.61%262/2257 |
| TP53 SNV / small indel | 11.54%57/494 | 18.56%188/1013 | 28.71%648/2257 |
| TP53 deep deletion | 4.29%21/489 | 1.97%20/1013 | 2.22%50/2257 |
| RB1 SNV / small indel | 0.61%3/494 | 1.48%15/1013 | 3.23%73/2257 |
| RB1 deep deletion | 9.41%46/489 | 4.05%41/1013 | 3.37%76/2257 |
| TMPRSS2 SNV / small indel | 0.81%4/494 | 0.89%9/1013 | 1.11%25/2257 |
| TMPRSS2 deep deletion | 11.86%58/489 | 0% | 1.06%24/2257 |
| ERG SNV / small indel | 0% | 0.39%4/1013 | 0.71%16/2257 |
| ERG deep deletion | 10.02%49/489 | 0% | 0% |
| SPOP SNV / small indel | 11.13%55/494 | 9.08%92/1013 | 14.09%318/2257 |
| KLK3 SNV / small indel | 0.81%4/494 | 0.59%6/1013 | · |
| KMT2D SNV / small indel | 5.67%28/494 | 6.42%65/1013 | 6.65%150/2257 |
| FOXA1 SNV / small indel | 5.67%28/494 | 6.81%69/1013 | 15.55%351/2257 |
| FOXA1 amplification | 3.07%15/489 | 3.16%32/1013 | 2.39%54/2257 |
| KMT2C SNV / small indel | 5.06%25/494 | 6.42%65/1013 | 6.82%154/2257 |
| CACNA1E SNV / small indel | 3.04%15/494 | 3.65%37/1013 | · |
| MYO15A SNV / small indel | 2.83%14/494 | 3.36%34/1013 | · |
| ZFHX3 SNV / small indel | 2.63%13/494 | 4.05%41/1013 | 6.64%141/2122 |
| ZFHX3 deep deletion | 5.93%29/489 | 0% | 2.35%53/2257 |
| DCHS2 SNV / small indel | 2.43%12/494 | 3.95%40/1013 | · |
| NALCN SNV / small indel | 2.23%11/494 | 1.88%19/1013 | · |
| GRIA1 SNV / small indel | 2.23%11/494 | 1.88%19/1013 | · |
| FBN1 SNV / small indel | 2.23%11/494 | 1.97%20/1013 | · |
| CTNNB1 SNV / small indel | 2.23%11/494 | 2.96%30/1013 | 3.94%89/2257 |
| ADGRB3 SNV / small indel | 2.23%11/494 | 2.37%24/1013 | · |
| ADGRB3 deep deletion | 3.68%18/489 | 2.96%30/1013 | 0% |
| ZMYM3 SNV / small indel | 2.02%10/494 | 1.68%17/1013 | · |
| SALL1 SNV / small indel | 2.02%10/494 | 1.58%16/1013 | · |
| SALL1 deep deletion | 2.04%10/489 | 0% | 0% |
| PIK3CA SNV / small indel | 2.02%10/494 | 2.86%29/1013 | 4.83%109/2257 |
| PIK3CA amplification | 2.25%11/489 | 4.05%41/1013 | 0.18%4/2257 |
| MXRA5 SNV / small indel | 2.02%10/494 | 1.88%19/1013 | · |
| FBN3 SNV / small indel | 2.02%10/494 | 2.07%21/1013 | · |
| EPB41L3 SNV / small indel | 2.02%10/494 | 1.48%15/1013 | · |
| CACNA1A SNV / small indel | 2.02%10/494 | 1.88%19/1013 | · |
| APC SNV / small indel | 2.02%10/494 | 3.26%33/1013 | 7.75%175/2257 |
| APC deep deletion | 2.45%12/489 | 1.78%18/1013 | 1.37%31/2257 |
| STAB2 SNV / small indel | 1.82%9/494 | 2.17%22/1013 | · |
| RNF213 SNV / small indel | 1.82%9/494 | 2.37%24/1013 | · |
| PCDH15 SNV / small indel | 1.82%9/494 | 2.76%28/1013 | · |
| NAV2 SNV / small indel | 1.82%9/494 | 2.37%24/1013 | · |
| MYH8 SNV / small indel | 1.82%9/494 | 1.48%15/1013 | · |
| LAMA3 SNV / small indel | 1.82%9/494 | 1.97%20/1013 | · |
| KDM6A SNV / small indel | 1.82%9/494 | 2.86%29/1013 | 3.59%81/2257 |
| HUWE1 SNV / small indel | 1.82%9/494 | 1.58%16/1013 | · |
| GRM1 SNV / small indel | 1.82%9/494 | 1.58%16/1013 | · |
| GRIN2A SNV / small indel | 1.82%9/494 | 2.67%27/1013 | 3.28%74/2257 |
| GAD2 SNV / small indel | 1.82%9/494 | 1.38%14/1013 | · |
| FCGBP SNV / small indel | 1.82%9/494 | 2.37%24/1013 | · |
| FAT2 SNV / small indel | 1.82%9/494 | 2.76%28/1013 | · |
| COL6A3 SNV / small indel | 1.82%9/494 | 1.97%20/1013 | · |
| CDK12 SNV / small indel | 1.82%9/494 | 3.16%32/1013 | 5.72%129/2257 |
| ADGRL3 SNV / small indel | 1.82%9/494 | 1.97%20/1013 | · |
| ADGRL3 deep deletion | 0.41%2/489 | 2.07%21/1013 | 0% |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
PTEN is deleted in 85 of 489 patients in Prostate Adenocarcinoma (TCGA, PanCancer Atlas).
TMPRSS2 is deleted in 58 of 489 patients in Prostate Adenocarcinoma (TCGA, PanCancer Atlas).
TP53 is mutated in 57 of 494 patients in Prostate Adenocarcinoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
Headline values are from the reference cohort, prad_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 |
|---|---|---|---|---|---|---|---|---|
| AR | curated target | amplification | 5 / 489 | 1.02% mutation 0.4% | 0.41% | 3 / 3 | 0.4–4.74% | A597T (n=1), R608Q (n=1) |
| FOLH1 | curated target | deep deletion | 2 / 489 | 0.41% mutation 0.0% | 0.0% | 1 / 3 | 0.0–0.1% | none recurrent |
| CYP17A1 | curated target | deep deletion | 6 / 489 | 1.23% mutation 0.2% | 0.0% | 2 / 3 | 0.2–0.2% | I104S (n=1) |
| BRCA2 | curated target | deep deletion | 17 / 489 | 3.48% mutation 1.62% | 1.43% | 3 / 3 | 1.62–3.99% | N433Tfs*27 (n=1), N1435T (n=1), V726Sfs*25 (n=1), S3364Ifs*4 (n=1), D281H (n=1) |
| ATM | curated target | SNV / small indel | 20 / 494 | 4.05% | 4.08% | 3 / 3 | 3.75–4.25% | G2695S (n=1), G1672A (n=1), E2164K (n=1), L1936S (n=1), W484* (n=1) |
| PTEN | curated target | deep deletion | 85 / 489 | 17.38% mutation 3.64% | 3.67% | 3 / 3 | 3.64–7.98% | T319Ffs*5 (n=1), V119F (n=1), D326G (n=1), X70_splice (n=1), L220Qfs*3 (n=1) |
| TP53 | curated target | SNV / small indel | 57 / 494 | 11.54% | 11.22% | 3 / 3 | 11.54–28.71% | R248Q (n=4), G245S (n=3), R175H (n=2), R282W (n=2), Y163H (n=2) |
| RB1 | curated target | deep deletion | 46 / 489 | 9.41% mutation 0.61% | 0.41% | 3 / 3 | 0.61–3.23% | F226L (n=1), X405_splice (n=1), G617Rfs*36 (n=1), L337Ffs*4 (n=1) |
| TMPRSS2 | curated target | deep deletion | 58 / 489 | 11.86% mutation 0.81% | 0.82% | 3 / 3 | 0.81–1.11% | E215K (n=1), S116* (n=1), K377Qfs*6 (n=1), N341del (n=1) |
| ERG | curated target | deep deletion | 49 / 489 | 10.02% mutation 0.0% | 0.0% | 2 / 3 | 0.0–0.71% | none recurrent |
| SPOP | curated target | SNV / small indel | 55 / 494 | 11.13% | 11.02% | 3 / 3 | 9.08–14.09% | W131G (n=8), F133L (n=7), F133V (n=6), F133C (n=4), F102V (n=4) |
| KLK3 | curated target | SNV / small indel | 4 / 494 | 0.81% | 0.82% | 2 / 3 | 0.59–0.81% | D102E (n=1), D182A (n=1), V42L (n=1), P129L (n=1) |
| KMT2D | by frequency | SNV / small indel | 28 / 494 | 5.67% | 5.31% | 3 / 3 | 5.67–6.65% | C5109F (n=1), E1167* (n=1), Q3394* (n=1), L2981V (n=1), E731Afs*17 (n=1) |
| FOXA1 | by frequency | SNV / small indel | 28 / 494 | 5.67% | 5.51% | 3 / 3 | 5.67–15.55% | F254_N256delinsY (n=3), E255_N256del (n=1), A423Dfs*17 (n=1), *473Eext*34 (n=1), M253T (n=1) |
| KMT2C | by frequency | SNV / small indel | 25 / 494 | 5.06% | 4.9% | 3 / 3 | 5.06–6.82% | Y4440C (n=2), E3726Kfs*20 (n=1), P3034Lfs*4 (n=1), E3937Kfs*6 (n=1), Q1872* (n=1) |
| CACNA1E | by frequency | SNV / small indel | 15 / 494 | 3.04% | 2.86% | 2 / 3 | 3.04–3.65% | V1976M (n=1), R1396H (n=1), V2162I (n=1), V1231I (n=1), R946C (n=1) |
| MYO15A | by frequency | SNV / small indel | 14 / 494 | 2.83% | 2.45% | 2 / 3 | 2.83–3.36% | R2262C (n=1), S1760Y (n=1), E313K (n=1), R950H (n=1), R192H (n=1) |
| ZFHX3 | by frequency | deep deletion | 29 / 489 | 5.93% mutation 2.63% | 2.04% | 3 / 3 | 2.63–6.64% | F1798Qfs*3 (n=1), R2998Q (n=1), L3355Afs*76 (n=1), G1901Rfs*14 (n=1), A776V (n=1) |
| DCHS2 | by frequency | SNV / small indel | 12 / 494 | 2.43% | 2.24% | 2 / 3 | 2.43–3.95% | F2421L (n=1), T1072I (n=1), R110Q (n=1), V526I (n=1), P1247T (n=1) |
| NALCN | by frequency | SNV / small indel | 11 / 494 | 2.23% | 1.84% | 2 / 3 | 1.88–2.23% | R295C (n=1), A860T (n=1), A277T (n=1), E161Q (n=1), G1013S (n=1) |
| GRIA1 | by frequency | SNV / small indel | 11 / 494 | 2.23% | 2.04% | 2 / 3 | 1.88–2.23% | R455H (n=2), R855W (n=2), K775I (n=1), T657K (n=1), V618I (n=1) |
| FBN1 | by frequency | SNV / small indel | 11 / 494 | 2.23% | 1.84% | 2 / 3 | 1.97–2.23% | C2000F (n=1), Y798C (n=1), L771Tfs*7 (n=1), E1366K (n=1), P1225L (n=1) |
| CTNNB1 | by frequency | SNV / small indel | 11 / 494 | 2.23% | 2.04% | 3 / 3 | 2.23–3.94% | T41A (n=2), D32V (n=1), D32H (n=1), S37A (n=1), D32Y (n=1) |
| ADGRB3 | by frequency | deep deletion | 18 / 489 | 3.68% mutation 2.23% | 2.24% | 2 / 3 | 2.23–2.37% | R588Q (n=1), W351L (n=1), D91N (n=1), S1176L (n=1), M1114L (n=1) |
| ZMYM3 | by frequency | SNV / small indel | 10 / 494 | 2.02% | 1.63% | 2 / 3 | 1.68–2.02% | X260_splice (n=1), Y1130* (n=1), P1296T (n=1), P1296R (n=1), N1154K (n=1) |
| SALL1 | by frequency | deep deletion | 10 / 489 | 2.04% mutation 2.02% | 1.84% | 2 / 3 | 1.58–2.02% | T745M (n=1), I343T (n=1), C717S (n=1), D814N (n=1), L1122P (n=1) |
| PIK3CA | by frequency | amplification | 11 / 489 | 2.25% mutation 2.02% | 1.84% | 3 / 3 | 2.02–4.83% | E542K (n=2), H1047R (n=2), *1069* (n=1), R88Q (n=1), N345K (n=1) |
| MXRA5 | by frequency | SNV / small indel | 10 / 494 | 2.02% | 1.84% | 2 / 3 | 1.88–2.02% | A254S (n=1), I2548Dfs*51 (n=1), T2106R (n=1), R1356H (n=1), R2297C (n=1) |
| FBN3 | by frequency | SNV / small indel | 10 / 494 | 2.02% | 1.84% | 2 / 3 | 2.02–2.07% | R1350C (n=1), C2526W (n=1), N1454K (n=1), R314C (n=1), C582S (n=1) |
| EPB41L3 | by frequency | SNV / small indel | 10 / 494 | 2.02% | 1.84% | 2 / 3 | 1.48–2.02% | I812T (n=1), K148T (n=1), T837M (n=1), R328Q (n=1), R694C (n=1) |
| CACNA1A | by frequency | SNV / small indel | 10 / 494 | 2.02% | 1.43% | 2 / 3 | 1.88–2.02% | T808M (n=1), T542M (n=1), E532K (n=1), V86M (n=1), T1676N (n=1) |
| APC | by frequency | deep deletion | 12 / 489 | 2.45% mutation 2.02% | 2.04% | 3 / 3 | 2.02–7.75% | S1539* (n=1), Q1123* (n=1), T1438Nfs*17 (n=1), R2714H (n=1), A1553V (n=1) |
| STAB2 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.43% | 2 / 3 | 1.82–2.17% | Y447C (n=1), H2138Y (n=1), R1940Q (n=1), E463K (n=1), A632T (n=1) |
| RNF213 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.22% | 2 / 3 | 1.82–2.37% | L2860Rfs*12 (n=1), Y1967C (n=1), A2849V (n=1), M4673I (n=1), V3581I (n=1) |
| PCDH15 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–2.76% | T1802K (n=1), P1420H (n=1), T301M (n=1), K1365N (n=1), P1631T (n=1) |
| NAV2 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–2.37% | A468G (n=1), E2100G (n=1), A1790S (n=1), P29Q (n=1), K1638E (n=1) |
| MYH8 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.48–1.82% | Q917H (n=1), V673A (n=1), A426V (n=1), G181R (n=1), Q1856R (n=1) |
| LAMA3 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.43% | 2 / 3 | 1.82–1.97% | R2402* (n=1), X2681_splice (n=1), T2980I (n=1), E1508* (n=1), P1658Lfs*91 (n=1) |
| KDM6A | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 3 / 3 | 1.82–3.59% | K987R (n=1), M1380Wfs*4 (n=1), X1392_splice (n=1), X1335_splice (n=1), N1117Y (n=1) |
| HUWE1 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.58–1.82% | R1894H (n=1), M1336V (n=1), R4007S (n=1), A3050V (n=1), R4122H (n=1) |
| GRM1 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.58–1.82% | R297* (n=2), R379C (n=1), R275H (n=1), R981C (n=1), R684C (n=1) |
| GRIN2A | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 3 / 3 | 1.82–3.28% | E1040D (n=1), E1123* (n=1), V109I (n=1), D973Y (n=1), F473I (n=1) |
| GAD2 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.38–1.82% | K222N (n=1), Y425* (n=1), G41R (n=1), G16D (n=1), N487Kfs*6 (n=1) |
| FCGBP | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–2.37% | G976D (n=1), V531I (n=1), N4006S (n=1), R5341C (n=1), R134W (n=1) |
| FAT2 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–2.76% | W4167Gfs*32 (n=1), H1551R (n=1), R308W (n=1), T3931M (n=1), G2251A (n=1) |
| COL6A3 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–1.97% | G1103E (n=1), V1885M (n=1), X2071_splice (n=1), P2232Q (n=1), S521L (n=1) |
| CDK12 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 3 / 3 | 1.82–5.72% | G1461Afs*38 (n=1), G1446E (n=1), R858W (n=1), S343Efs*8 (n=1), Q598* (n=1) |
| ADGRL3 | by frequency | SNV / small indel | 9 / 494 | 1.82% | 1.63% | 2 / 3 | 1.82–1.97% | R826H (n=2), R234W (n=1), W832L (n=1), I409N (n=1), R1139* (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 |
|---|---|---|---|---|---|---|---|---|---|
| Prostate Adenocarcinoma (TCGA, PanCancer Atlas) reference | prad_tcga_pan_can_atlas_2018 | 494 observed | 494 / 494 | exome or genome | WES (494) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 4 | 26.0 |
| Prostate Adenocarcinoma (MSK/DFCI, Nature Genetics 2018) | prad_p1000 | 1013 observed | 1013 / 1013 | exome or genome | WES (1013) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 18 | 30 |
| Prostate Cancer (MSK, Clin Cancer Res 2024) | prostate_msk_2024 | 2257 observed | 2260 / 2260 | targeted panel | IMPACT468 (1477), IMPACT410 (480), IMPACT505 (167), IMPACT341 (136) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 4 | 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 |
|---|---|---|---|---|---|---|
| PTEN | deep deletion | 85 | 489 | 17.38% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| AR | amplification | 127 | 1013 | 12.54% | prad_p1000 | prad_p1000_cna |
| PTEN | deep deletion | 124 | 1013 | 12.24% | prad_p1000 | prad_p1000_cna |
| TMPRSS2 | deep deletion | 58 | 489 | 11.86% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| PTEN | deep deletion | 262 | 2257 | 11.61% | prostate_msk_2024 | prostate_msk_2024_cna |
| AR | amplification | 236 | 2257 | 10.46% | prostate_msk_2024 | prostate_msk_2024_cna |
| ERG | deep deletion | 49 | 489 | 10.02% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 46 | 489 | 9.41% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| ZFHX3 | deep deletion | 29 | 489 | 5.93% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| TP53 | deep deletion | 21 | 489 | 4.29% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 41 | 1013 | 4.05% | prad_p1000 | prad_p1000_cna |
| PIK3CA | amplification | 41 | 1013 | 4.05% | prad_p1000 | prad_p1000_cna |
| ADGRB3 | deep deletion | 18 | 489 | 3.68% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| BRCA2 | deep deletion | 17 | 489 | 3.48% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 76 | 2257 | 3.37% | prostate_msk_2024 | prostate_msk_2024_cna |
| FOXA1 | amplification | 32 | 1013 | 3.16% | prad_p1000 | prad_p1000_cna |
| FOXA1 | amplification | 15 | 489 | 3.07% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| ADGRB3 | deep deletion | 30 | 1013 | 2.96% | prad_p1000 | prad_p1000_cna |
| BRCA2 | deep deletion | 25 | 1013 | 2.47% | prad_p1000 | prad_p1000_cna |
| APC | deep deletion | 12 | 489 | 2.45% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| FOXA1 | amplification | 54 | 2257 | 2.39% | prostate_msk_2024 | prostate_msk_2024_cna |
| ZFHX3 | deep deletion | 53 | 2257 | 2.35% | prostate_msk_2024 | prostate_msk_2024_cna |
| PIK3CA | amplification | 11 | 489 | 2.25% | prad_tcga_pan_can_atlas_2018 | prad_tcga_pan_can_atlas_2018_gistic |
| TP53 | deep deletion | 50 | 2257 | 2.22% | prostate_msk_2024 | prostate_msk_2024_cna |
| FOLH1 | deep deletion | 22 | 1013 | 2.17% | prad_p1000 | prad_p1000_cna |
| BRCA2 | deep deletion | 49 | 2257 | 2.17% | prostate_msk_2024 | prostate_msk_2024_cna |
| ADGRL3 | deep deletion | 21 | 1013 | 2.07% | prad_p1000 | prad_p1000_cna |
| SALL1 | deep deletion | 10 | 489 | 2.04% | prad_tcga_pan_can_atlas_2018 | prad_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) |
|---|---|---|
| AR | 0.4–4.74% | prad_tcga_pan_can_atlas_2018: 2/494 (0.4%) · prad_p1000: 48/1013 (4.74%) · prostate_msk_2024: 93/2257 (4.12%) |
| FOLH1 | 0.0–0.1% | prad_tcga_pan_can_atlas_2018: 0/494 (0.0%) · prad_p1000: 1/1013 (0.1%) · prostate_msk_2024: not assayed |
| CYP17A1 | 0.2–0.2% | prad_tcga_pan_can_atlas_2018: 1/494 (0.2%) · prad_p1000: 2/1013 (0.2%) · prostate_msk_2024: not assayed |
| BRCA2 | 1.62–3.99% | prad_tcga_pan_can_atlas_2018: 8/494 (1.62%) · prad_p1000: 29/1013 (2.86%) · prostate_msk_2024: 90/2257 (3.99%) |
| ATM | 3.75–4.25% | prad_tcga_pan_can_atlas_2018: 20/494 (4.05%) · prad_p1000: 38/1013 (3.75%) · prostate_msk_2024: 96/2257 (4.25%) |
| PTEN | 3.64–7.98% | prad_tcga_pan_can_atlas_2018: 18/494 (3.64%) · prad_p1000: 43/1013 (4.24%) · prostate_msk_2024: 180/2257 (7.98%) |
| TP53 | 11.54–28.71% | prad_tcga_pan_can_atlas_2018: 57/494 (11.54%) · prad_p1000: 188/1013 (18.56%) · prostate_msk_2024: 648/2257 (28.71%) |
| RB1 | 0.61–3.23% | prad_tcga_pan_can_atlas_2018: 3/494 (0.61%) · prad_p1000: 15/1013 (1.48%) · prostate_msk_2024: 73/2257 (3.23%) |
| TMPRSS2 | 0.81–1.11% | prad_tcga_pan_can_atlas_2018: 4/494 (0.81%) · prad_p1000: 9/1013 (0.89%) · prostate_msk_2024: 25/2257 (1.11%) |
| ERG | 0.0–0.71% | prad_tcga_pan_can_atlas_2018: 0/494 (0.0%) · prad_p1000: 4/1013 (0.39%) · prostate_msk_2024: 16/2257 (0.71%) |
| SPOP | 9.08–14.09% | prad_tcga_pan_can_atlas_2018: 55/494 (11.13%) · prad_p1000: 92/1013 (9.08%) · prostate_msk_2024: 318/2257 (14.09%) |
| KLK3 | 0.59–0.81% | prad_tcga_pan_can_atlas_2018: 4/494 (0.81%) · prad_p1000: 6/1013 (0.59%) · prostate_msk_2024: not assayed |
| KMT2D | 5.67–6.65% | prad_tcga_pan_can_atlas_2018: 28/494 (5.67%) · prad_p1000: 65/1013 (6.42%) · prostate_msk_2024: 150/2257 (6.65%) |
| FOXA1 | 5.67–15.55% | prad_tcga_pan_can_atlas_2018: 28/494 (5.67%) · prad_p1000: 69/1013 (6.81%) · prostate_msk_2024: 351/2257 (15.55%) |
| KMT2C | 5.06–6.82% | prad_tcga_pan_can_atlas_2018: 25/494 (5.06%) · prad_p1000: 65/1013 (6.42%) · prostate_msk_2024: 154/2257 (6.82%) |
| CACNA1E | 3.04–3.65% | prad_tcga_pan_can_atlas_2018: 15/494 (3.04%) · prad_p1000: 37/1013 (3.65%) · prostate_msk_2024: not assayed |
| MYO15A | 2.83–3.36% | prad_tcga_pan_can_atlas_2018: 14/494 (2.83%) · prad_p1000: 34/1013 (3.36%) · prostate_msk_2024: not assayed |
| ZFHX3 | 2.63–6.64% | prad_tcga_pan_can_atlas_2018: 13/494 (2.63%) · prad_p1000: 41/1013 (4.05%) · prostate_msk_2024: 141/2122 (6.64%) |
| DCHS2 | 2.43–3.95% | prad_tcga_pan_can_atlas_2018: 12/494 (2.43%) · prad_p1000: 40/1013 (3.95%) · prostate_msk_2024: not assayed |
| NALCN | 1.88–2.23% | prad_tcga_pan_can_atlas_2018: 11/494 (2.23%) · prad_p1000: 19/1013 (1.88%) · prostate_msk_2024: not assayed |
| GRIA1 | 1.88–2.23% | prad_tcga_pan_can_atlas_2018: 11/494 (2.23%) · prad_p1000: 19/1013 (1.88%) · prostate_msk_2024: not assayed |
| FBN1 | 1.97–2.23% | prad_tcga_pan_can_atlas_2018: 11/494 (2.23%) · prad_p1000: 20/1013 (1.97%) · prostate_msk_2024: not assayed |
| CTNNB1 | 2.23–3.94% | prad_tcga_pan_can_atlas_2018: 11/494 (2.23%) · prad_p1000: 30/1013 (2.96%) · prostate_msk_2024: 89/2257 (3.94%) |
| ADGRB3 | 2.23–2.37% | prad_tcga_pan_can_atlas_2018: 11/494 (2.23%) · prad_p1000: 24/1013 (2.37%) · prostate_msk_2024: not assayed |
| ZMYM3 | 1.68–2.02% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 17/1013 (1.68%) · prostate_msk_2024: not assayed |
| SALL1 | 1.58–2.02% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 16/1013 (1.58%) · prostate_msk_2024: not assayed |
| PIK3CA | 2.02–4.83% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 29/1013 (2.86%) · prostate_msk_2024: 109/2257 (4.83%) |
| MXRA5 | 1.88–2.02% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 19/1013 (1.88%) · prostate_msk_2024: not assayed |
| FBN3 | 2.02–2.07% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 21/1013 (2.07%) · prostate_msk_2024: not assayed |
| EPB41L3 | 1.48–2.02% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 15/1013 (1.48%) · prostate_msk_2024: not assayed |
| CACNA1A | 1.88–2.02% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 19/1013 (1.88%) · prostate_msk_2024: not assayed |
| APC | 2.02–7.75% | prad_tcga_pan_can_atlas_2018: 10/494 (2.02%) · prad_p1000: 33/1013 (3.26%) · prostate_msk_2024: 175/2257 (7.75%) |
| STAB2 | 1.82–2.17% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 22/1013 (2.17%) · prostate_msk_2024: not assayed |
| RNF213 | 1.82–2.37% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 24/1013 (2.37%) · prostate_msk_2024: not assayed |
| PCDH15 | 1.82–2.76% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 28/1013 (2.76%) · prostate_msk_2024: not assayed |
| NAV2 | 1.82–2.37% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 24/1013 (2.37%) · prostate_msk_2024: not assayed |
| MYH8 | 1.48–1.82% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 15/1013 (1.48%) · prostate_msk_2024: not assayed |
| LAMA3 | 1.82–1.97% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 20/1013 (1.97%) · prostate_msk_2024: not assayed |
| KDM6A | 1.82–3.59% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 29/1013 (2.86%) · prostate_msk_2024: 81/2257 (3.59%) |
| HUWE1 | 1.58–1.82% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 16/1013 (1.58%) · prostate_msk_2024: not assayed |
| GRM1 | 1.58–1.82% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 16/1013 (1.58%) · prostate_msk_2024: not assayed |
| GRIN2A | 1.82–3.28% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 27/1013 (2.67%) · prostate_msk_2024: 74/2257 (3.28%) |
| GAD2 | 1.38–1.82% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 14/1013 (1.38%) · prostate_msk_2024: not assayed |
| FCGBP | 1.82–2.37% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 24/1013 (2.37%) · prostate_msk_2024: not assayed |
| FAT2 | 1.82–2.76% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 28/1013 (2.76%) · prostate_msk_2024: not assayed |
| COL6A3 | 1.82–1.97% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 20/1013 (1.97%) · prostate_msk_2024: not assayed |
| CDK12 | 1.82–5.72% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 32/1013 (3.16%) · prostate_msk_2024: 129/2257 (5.72%) |
| ADGRL3 | 1.82–1.97% | prad_tcga_pan_can_atlas_2018: 9/494 (1.82%) · prad_p1000: 20/1013 (1.97%) · prostate_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 2026-09-18; the page does not refresh source data at request time.
- Counts are patients with at least one non-silent call in the study's sequenced sample list; silent, intronic and UTR calls are excluded.
- For targeted-panel cohorts each gene divides by the patients whose panel carried it; a gene absent from the panel is shown as not assayed, not as zero.
- Copy-number rows use discrete calls (2 = high-level amplification, −2 = deep deletion) against the cohort's copy-number sample list, which is a different roster from the sequenced one.
- Cohorts are not pooled. Cross-study patient overlap has not been checked and no disease-wide frequency is reported.
- Structural variants and fusions are not read in this snapshot even where the study carries a profile; germline variants, mutational signatures, TMB and MSI are not reported.
- The gene set is the briefing's curated targets plus the reference cohort's most frequently mutated genes; it is not genome-wide.
How a machine should read this page
- Denominators: every frequency divides by the patients in one named cohort on whom the gene could be called; there is no disease-wide figure.
- Missing values:
not_assayed(the panel did not carry the gene),not_observed(assayed, none found) andnot_evaluable(the cohort could not be read) are three different facts and are never converted to zero. - Counting: patients, not samples; several samples from one patient count once. Non-silent calls only.
- Copy number: a separate assay with a separate roster; discrete calls at ±2 only.
- Hypermutation: flagged per cohort; the headline keeps all patients and the frequency without them is reported beside it.
- Provenance: every value carries the study id, the retrieval date and the processing version; the source is the cBioPortal public API.
Machine endpoints: full landscape · genes · cohorts · the disease's own facts: /disease/prostate-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.