Disease intelligence · mutation landscape
Breast cancer mutation landscape
How often each gene is altered in breast 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 TCGA PanCancer Atlas breast (2018) (1066 sequenced patients, exome or genome), the most frequently altered of the 47 genes shown are PIK3CA 32.46%, TP53 32.46%, GATA3 11.91%, CDH1 11.91%, ERBB2 11.5% (amplification). Each figure divides by the patients on whom that gene could be called.
21 of 1066 patients are hypermutated (more than 370 non-silent mutations, ten times the cohort median of 37); every gene's frequency without them is beside the headline.
Of the briefing's 12 curated targets, 5 are altered in under 2% of this cohort (ESR1, PGR, CDK4, CDK6, TACSTD2): 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 | brca_tcga_pan_can_atlas_2018 1066 pts · exome or genome | brca_metabric 2433 pts · targeted panel | brca_msk_2025 462 pts · targeted panel |
|---|---|---|---|
| ESR1 SNV / small indel | 0.84%9/1066 | · | 14.07%65/462 |
| ESR1 amplification | 1.87%20/1070 | 2.3%50/2173 | 2.16%10/462 |
| PGR SNV / small indel | 0.66%7/1066 | · | 3.5%15/429 |
| ERBB2 SNV / small indel | 2.81%30/1066 | 2.92%71/2433 | 10.39%48/462 |
| ERBB2 amplification | 11.5%123/1070 | 15.74%342/2173 | 14.5%67/462 |
| PIK3CA SNV / small indel | 32.46%346/1066 | 40.07%975/2433 | 59.96%277/462 |
| PIK3CA amplification | 3.18%34/1070 | 4.51%98/2173 | 3.25%15/462 |
| AKT1 SNV / small indel | 2.53%27/1066 | 4.03%98/2433 | 6.49%30/462 |
| PTEN SNV / small indel | 5.44%58/1066 | 3.9%95/2433 | 14.29%66/462 |
| PTEN deep deletion | 5.14%55/1070 | 2.02%44/2173 | 1.52%7/462 |
| CDK4 SNV / small indel | 0% | · | 1.08%5/462 |
| CDK6 SNV / small indel | 0.28%3/1066 | · | 0.87%4/462 |
| BRCA1 SNV / small indel | 2.53%27/1066 | 1.73%42/2433 | 8.01%37/462 |
| BRCA2 SNV / small indel | 2.72%29/1066 | 1.85%45/2433 | 12.12%56/462 |
| TP53 SNV / small indel | 32.46%346/1066 | 35.39%861/2433 | 55.84%258/462 |
| TACSTD2 SNV / small indel | 0% | · | · |
| GATA3 SNV / small indel | 11.91%127/1066 | 10.97%267/2433 | 13.64%63/462 |
| GATA3 amplification | 2.99%32/1070 | 4.65%101/2173 | 2.16%10/462 |
| CDH1 SNV / small indel | 11.91%127/1066 | 9.58%233/2433 | 30.74%142/462 |
| KMT2C SNV / small indel | 9.1%97/1066 | 11.39%277/2433 | 27.92%129/462 |
| MAP3K1 SNV / small indel | 8.35%89/1066 | 9.7%236/2433 | 17.75%82/462 |
| NCOR1 SNV / small indel | 4.69%50/1066 | 3.53%86/2433 | 14.07%65/462 |
| MAP2K4 SNV / small indel | 3.94%42/1066 | 3.25%79/2433 | 7.79%36/462 |
| MAP2K4 deep deletion | 2.43%26/1070 | 2.12%46/2173 | 1.52%7/462 |
| RUNX1 SNV / small indel | 3.75%40/1066 | 3.33%81/2433 | 5.41%25/462 |
| RUNX1 amplification | 1.21%13/1070 | 2.39%52/2173 | 0.22%1/462 |
| ARID1A SNV / small indel | 3.66%39/1066 | 4.69%114/2433 | 17.75%82/462 |
| HUWE1 SNV / small indel | 3.56%38/1066 | · | · |
| NF1 SNV / small indel | 3.47%37/1066 | 3.74%91/2433 | 20.56%95/462 |
| NF1 amplification | 2.24%24/1070 | 1.61%35/2173 | 0.43%2/462 |
| CACNA1E SNV / small indel | 3.47%37/1066 | · | · |
| CACNA1E amplification | 7.38%79/1070 | 20.94%455/2173 | 0% |
| MDN1 SNV / small indel | 3.38%36/1066 | · | · |
| RELN SNV / small indel | 3.19%34/1066 | · | · |
| TBX3 SNV / small indel | 3.1%33/1066 | 5.01%122/2433 | 13.2%61/462 |
| MYCBP2 SNV / small indel | 3.1%33/1066 | · | · |
| SPEN SNV / small indel | 3.0%32/1066 | · | 15.8%73/462 |
| KMT2D SNV / small indel | 3.0%32/1066 | 7.23%176/2433 | 20.56%95/462 |
| PRUNE2 SNV / small indel | 2.91%31/1066 | · | · |
| FOXA1 SNV / small indel | 2.91%31/1066 | · | 14.72%68/462 |
| FOXA1 amplification | 1.5%16/1070 | 2.25%49/2173 | 1.95%9/462 |
| FAT1 SNV / small indel | 2.91%31/1066 | · | 16.88%78/462 |
| VPS13C SNV / small indel | 2.81%30/1066 | · | · |
| TEX15 SNV / small indel | 2.81%30/1066 | · | · |
| TEX15 deep deletion | 3.64%39/1070 | 0.74%16/2173 | 0% |
| MYH9 SNV / small indel | 2.81%30/1066 | 3.58%87/2433 | · |
| MXRA5 SNV / small indel | 2.81%30/1066 | · | · |
| LYST SNV / small indel | 2.81%30/1066 | · | · |
| LYST amplification | 9.63%103/1070 | 21.54%468/2173 | 0% |
| FCGBP SNV / small indel | 2.81%30/1066 | · | · |
| FCGBP amplification | 2.15%23/1070 | 1.24%27/2173 | 0% |
| DYNC1H1 SNV / small indel | 2.81%30/1066 | · | · |
| BLTP1 SNV / small indel | 2.81%30/1066 | · | · |
| AKAP9 SNV / small indel | 2.81%30/1066 | 5.88%143/2433 | · |
| VPS13B SNV / small indel | 2.72%29/1066 | · | · |
| VPS13B amplification | 11.03%118/1070 | 20.94%455/2173 | 0% |
| UTRN SNV / small indel | 2.72%29/1066 | 5.01%122/2433 | · |
| PIK3R1 SNV / small indel | 2.72%29/1066 | 2.47%60/2433 | 6.49%30/462 |
| MED12 SNV / small indel | 2.72%29/1066 | · | 6.71%31/462 |
| HERC2 SNV / small indel | 2.72%29/1066 | 6.45%157/2433 | · |
| TG SNV / small indel | 2.63%28/1066 | 5.55%135/2433 | · |
| TG amplification | 11.31%121/1070 | 23.1%502/2173 | 0% |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
PIK3CA is mutated in 346 of 1066 patients in TCGA PanCancer Atlas breast (2018).
TP53 is mutated in 346 of 1066 patients in TCGA PanCancer Atlas breast (2018).
GATA3 is mutated in 127 of 1066 patients in TCGA PanCancer Atlas breast (2018).
Gene table — reference cohort
Headline values are from the reference cohort, brca_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 |
|---|---|---|---|---|---|---|---|---|
| ESR1 | curated target | amplification | 20 / 1070 | 1.87% mutation 0.84% | 0.57% | 2 / 3 | 0.84–14.07% | E380Q (n=2), A593D (n=1), E523Q (n=1), I451_I452del (n=1), P222S (n=1) |
| PGR | curated target | deep deletion | 10 / 1070 | 0.93% mutation 0.66% | 0.57% | 2 / 3 | 0.66–3.5% | R740Q (n=1), A914V (n=1), E596Gfs*13 (n=1), E833K (n=1), I896M (n=1) |
| ERBB2 | curated target | amplification | 123 / 1070 | 11.5% mutation 2.81% | 2.3% | 3 / 3 | 2.81–10.39% | L755S (n=5), V777L (n=4), D769Y (n=2), I767M (n=2), L755M (n=1) |
| PIK3CA | curated target | SNV / small indel | 346 / 1066 | 32.46% | 31.96% | 3 / 3 | 32.46–59.96% | H1047R (n=129), E545K (n=65), E542K (n=43), N345K (n=18), H1047L (n=13) |
| AKT1 | curated target | SNV / small indel | 27 / 1066 | 2.53% | 2.58% | 3 / 3 | 2.53–6.49% | E17K (n=25), L52R (n=1), V4L (n=1) |
| PTEN | curated target | SNV / small indel | 58 / 1066 | 5.44% | 4.59% | 3 / 3 | 3.9–14.29% | R130Q (n=4), R130* (n=2), T319* (n=2), K267Rfs*9 (n=2), N48Tfs*6 (n=2) |
| CDK4 | curated target | amplification | 14 / 1070 | 1.31% mutation 0.0% | 0.0% | 1 / 3 | 0.0–1.08% | none recurrent |
| CDK6 | curated target | amplification | 6 / 1070 | 0.56% mutation 0.28% | 0.19% | 2 / 3 | 0.28–0.87% | T88A (n=1), H139Q (n=1), P118S (n=1) |
| BRCA1 | curated target | SNV / small indel | 27 / 1066 | 2.53% | 2.2% | 3 / 3 | 1.73–8.01% | Q934* (n=1), E9Q (n=1), X27_splice (n=1), E720* (n=1), T688Vfs*12 (n=1) |
| BRCA2 | curated target | SNV / small indel | 29 / 1066 | 2.72% | 2.3% | 3 / 3 | 1.85–12.12% | Q3206E (n=1), Y3308* (n=1), L2926* (n=1), D1355Y (n=1), E260Sfs*15 (n=1) |
| TP53 | curated target | SNV / small indel | 346 / 1066 | 32.46% | 32.54% | 3 / 3 | 32.46–55.84% | R175H (n=21), R273H (n=13), R196* (n=8), Y220C (n=7), R342* (n=7) |
| TACSTD2 | curated target | amplification | 16 / 1070 | 1.5% mutation 0.0% | 0.0% | 0 / 3 | 0.0–0.0% | none recurrent |
| GATA3 | by frequency | SNV / small indel | 127 / 1066 | 11.91% | 11.67% | 3 / 3 | 10.97–13.64% | X308_splice (n=21), P408Afs*99 (n=13), D335Gfs*17 (n=8), M293K (n=3), S436Lfs*71 (n=2) |
| CDH1 | by frequency | SNV / small indel | 127 / 1066 | 11.91% | 11.58% | 3 / 3 | 9.58–30.74% | Q23* (n=8), R63* (n=4), P127Afs*41 (n=4), E243K (n=3), X722_splice (n=3) |
| KMT2C | by frequency | SNV / small indel | 97 / 1066 | 9.1% | 8.23% | 3 / 3 | 9.1–27.92% | R4478* (n=2), E640* (n=2), Q1478* (n=2), S1334C (n=1), E2838K (n=1) |
| MAP3K1 | by frequency | SNV / small indel | 89 / 1066 | 8.35% | 8.23% | 3 / 3 | 8.35–17.75% | R273Sfs*27 (n=3), R763Cfs*35 (n=3), V1346del (n=2), L319Tfs*7 (n=2), Q1048* (n=2) |
| NCOR1 | by frequency | SNV / small indel | 50 / 1066 | 4.69% | 4.21% | 3 / 3 | 3.53–14.07% | T525Nfs*11 (n=2), P7S (n=1), E531Q (n=1), G1163D (n=1), E592* (n=1) |
| MAP2K4 | by frequency | SNV / small indel | 42 / 1066 | 3.94% | 4.02% | 3 / 3 | 3.25–7.79% | R281* (n=2), S251I (n=2), X75_splice (n=2), D263Cfs*4 (n=2), S184L (n=2) |
| RUNX1 | by frequency | SNV / small indel | 40 / 1066 | 3.75% | 3.54% | 3 / 3 | 3.33–5.41% | D123Gfs*15 (n=5), R169Kfs*44 (n=2), D123Gfs*11 (n=2), D123Mfs*10 (n=1), A244V (n=1) |
| ARID1A | by frequency | SNV / small indel | 39 / 1066 | 3.66% | 3.35% | 3 / 3 | 3.66–17.75% | X960_splice (n=2), R1989* (n=2), Q528* (n=2), Q944* (n=1), R2143C (n=1) |
| HUWE1 | by frequency | SNV / small indel | 38 / 1066 | 3.56% | 2.49% | 1 / 3 | 3.56–3.56% | S3122F (n=1), A889T (n=1), R3174H (n=1), D882N (n=1), R3786Q (n=1) |
| NF1 | by frequency | SNV / small indel | 37 / 1066 | 3.47% | 3.06% | 3 / 3 | 3.47–20.56% | Q209* (n=1), W571* (n=1), R366* (n=1), E524Q (n=1), R2119Qfs*10 (n=1) |
| CACNA1E | by frequency | amplification | 79 / 1070 | 7.38% mutation 3.47% | 2.87% | 1 / 3 | 3.47–3.47% | R384C (n=2), R1396C (n=1), G2125V (n=1), Q110K (n=1), X391_splice (n=1) |
| MDN1 | by frequency | SNV / small indel | 36 / 1066 | 3.38% | 2.58% | 1 / 3 | 3.38–3.38% | L423F (n=1), K4830N (n=1), E2201Q (n=1), D2612H (n=1), D5539G (n=1) |
| RELN | by frequency | SNV / small indel | 34 / 1066 | 3.19% | 2.49% | 1 / 3 | 3.19–3.19% | G3444E (n=1), R1385I (n=1), F1269C (n=1), G2175S (n=1), D1175H (n=1) |
| TBX3 | by frequency | SNV / small indel | 33 / 1066 | 3.1% | 2.87% | 3 / 3 | 3.1–13.2% | H187Y (n=2), Y265Lfs*12 (n=1), P134S (n=1), M184Gfs*25 (n=1), K175* (n=1) |
| MYCBP2 | by frequency | SNV / small indel | 33 / 1066 | 3.1% | 2.3% | 1 / 3 | 3.1–3.1% | K2740M (n=1), I3077V (n=1), Q3845* (n=1), S143* (n=1), H3616Y (n=1) |
| SPEN | by frequency | SNV / small indel | 32 / 1066 | 3.0% | 2.2% | 2 / 3 | 3.0–15.8% | N1429K (n=1), P2059Kfs*3 (n=1), F609Lfs*2 (n=1), E2846K (n=1), E2201Q (n=1) |
| KMT2D | by frequency | SNV / small indel | 32 / 1066 | 3.0% | 2.11% | 3 / 3 | 3.0–20.56% | K1686Nfs*36 (n=2), T1681N (n=1), P3246Tfs*5 (n=1), E3587V (n=1), A2119Rfs*36 (n=1) |
| PRUNE2 | by frequency | SNV / small indel | 31 / 1066 | 2.91% | 2.11% | 1 / 3 | 2.91–2.91% | S576N (n=1), H2092Y (n=1), D830V (n=1), V2775M (n=1), S2432F (n=1) |
| FOXA1 | by frequency | SNV / small indel | 31 / 1066 | 2.91% | 2.68% | 2 / 3 | 2.91–14.72% | S250F (n=3), I176M (n=3), D226G (n=2), S194Afs*127 (n=1), I450M (n=1) |
| FAT1 | by frequency | SNV / small indel | 31 / 1066 | 2.91% | 2.11% | 2 / 3 | 2.91–16.88% | S2060F (n=2), T2261M (n=1), D2373N (n=1), K1044R (n=1), D2076N (n=1) |
| VPS13C | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 1.91% | 1 / 3 | 2.81–2.81% | T3732M (n=2), V3571I (n=1), E1451K (n=1), A840D (n=1), A1513S (n=1) |
| TEX15 | by frequency | deep deletion | 39 / 1070 | 3.64% mutation 2.81% | 2.49% | 1 / 3 | 2.81–2.81% | L2764F (n=1), S1432T (n=1), P1734L (n=1), T208K (n=1), E57Q (n=1) |
| MYH9 | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 2.3% | 2 / 3 | 2.81–3.58% | E530K (n=2), P726S (n=1), E1011Q (n=1), A1659T (n=1), L92V (n=1) |
| MXRA5 | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 2.11% | 1 / 3 | 2.81–2.81% | G798S (n=1), G473S (n=1), M273I (n=1), A1492G (n=1), E266* (n=1) |
| LYST | by frequency | amplification | 103 / 1070 | 9.63% mutation 2.81% | 2.01% | 1 / 3 | 2.81–2.81% | Q3352P (n=1), Q2237* (n=1), E1095K (n=1), V1744F (n=1), C2828* (n=1) |
| FCGBP | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 2.2% | 1 / 3 | 2.81–2.81% | N4225Tfs*173 (n=2), L1156R (n=1), G4218S (n=1), V3268I (n=1), E2651K (n=1) |
| DYNC1H1 | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 1.82% | 1 / 3 | 2.81–2.81% | K4418N (n=1), E1786K (n=1), V3797L (n=1), E4439G (n=1), V88I (n=1) |
| BLTP1 | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 2.39% | 1 / 3 | 2.81–2.81% | R3026T (n=1), R2025K (n=1), R3280Kfs*10 (n=1), E299* (n=1), E2425A (n=1) |
| AKAP9 | by frequency | SNV / small indel | 30 / 1066 | 2.81% | 2.3% | 2 / 3 | 2.81–5.88% | G3802* (n=1), E756Kfs*9 (n=1), T1942I (n=1), S3576Y (n=1), E3074Q (n=1) |
| VPS13B | by frequency | amplification | 118 / 1070 | 11.03% mutation 2.72% | 2.11% | 1 / 3 | 2.72–2.72% | G567E (n=1), I737T (n=1), V840M (n=1), P721T (n=1), G2706V (n=1) |
| UTRN | by frequency | SNV / small indel | 29 / 1066 | 2.72% | 1.91% | 2 / 3 | 2.72–5.01% | R2739T (n=1), D808H (n=1), E2888K (n=1), Q750E (n=1), E1688Q (n=1) |
| PIK3R1 | by frequency | SNV / small indel | 29 / 1066 | 2.72% | 2.39% | 3 / 3 | 2.47–6.49% | K567_L570del (n=3), K575_T576dup (n=1), E468_E469insGLYE (n=1), K459_S460dup (n=1), L380del (n=1) |
| MED12 | by frequency | SNV / small indel | 29 / 1066 | 2.72% | 2.3% | 2 / 3 | 2.72–6.71% | Q2159R (n=1), Q323* (n=1), F833L (n=1), K174N (n=1), D234V (n=1) |
| HERC2 | by frequency | SNV / small indel | 29 / 1066 | 2.72% | 1.91% | 2 / 3 | 2.72–6.45% | R1744* (n=1), L294_L296del (n=1), I1210M (n=1), G3189E (n=1), G279V (n=1) |
| TG | by frequency | amplification | 121 / 1070 | 11.31% mutation 2.63% | 2.11% | 2 / 3 | 2.63–5.55% | S1139L (n=1), W1554C (n=1), D1628Y (n=1), G1045R (n=1), Q1741H (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 breast (2018) reference | brca_tcga_pan_can_atlas_2018 | 1066 observed | 1066 / 1084 | exome or genome | WES (1066) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 21 | 37.0 |
| METABRIC (Nature 2012, Nat Commun 2016) | brca_metabric | 2433 observed | 2433 / 2509 | targeted panel | METABRIC_173 (2433) | hg19 | SNV, small indel, amplification, deep deletion | 0 | 5 |
| MSK breast carcinoma (2025) | brca_msk_2025 | 462 observed | 527 / 527 | targeted panel | IMPACT468 (283), IMPACT505 (124), IMPACT410 (81), IMPACT341 (39) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 2 | 16 |
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 |
|---|---|---|---|---|---|---|
| TG | amplification | 502 | 2173 | 23.1% | brca_metabric | brca_metabric_cna |
| LYST | amplification | 468 | 2173 | 21.54% | brca_metabric | brca_metabric_cna |
| CACNA1E | amplification | 455 | 2173 | 20.94% | brca_metabric | brca_metabric_cna |
| VPS13B | amplification | 455 | 2173 | 20.94% | brca_metabric | brca_metabric_cna |
| ERBB2 | amplification | 342 | 2173 | 15.74% | brca_metabric | brca_metabric_cna |
| ERBB2 | amplification | 67 | 462 | 14.5% | brca_msk_2025 | brca_msk_2025_gistic |
| ERBB2 | amplification | 123 | 1070 | 11.5% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| TG | amplification | 121 | 1070 | 11.31% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| VPS13B | amplification | 118 | 1070 | 11.03% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| LYST | amplification | 103 | 1070 | 9.63% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| CACNA1E | amplification | 79 | 1070 | 7.38% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| PTEN | deep deletion | 55 | 1070 | 5.14% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| GATA3 | amplification | 101 | 2173 | 4.65% | brca_metabric | brca_metabric_cna |
| PIK3CA | amplification | 98 | 2173 | 4.51% | brca_metabric | brca_metabric_cna |
| TEX15 | deep deletion | 39 | 1070 | 3.64% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| PIK3CA | amplification | 15 | 462 | 3.25% | brca_msk_2025 | brca_msk_2025_gistic |
| PIK3CA | amplification | 34 | 1070 | 3.18% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| GATA3 | amplification | 32 | 1070 | 2.99% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| MAP2K4 | deep deletion | 26 | 1070 | 2.43% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| RUNX1 | amplification | 52 | 2173 | 2.39% | brca_metabric | brca_metabric_cna |
| ESR1 | amplification | 50 | 2173 | 2.3% | brca_metabric | brca_metabric_cna |
| FOXA1 | amplification | 49 | 2173 | 2.25% | brca_metabric | brca_metabric_cna |
| NF1 | amplification | 24 | 1070 | 2.24% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| ESR1 | amplification | 10 | 462 | 2.16% | brca_msk_2025 | brca_msk_2025_gistic |
| GATA3 | amplification | 10 | 462 | 2.16% | brca_msk_2025 | brca_msk_2025_gistic |
| FCGBP | amplification | 23 | 1070 | 2.15% | brca_tcga_pan_can_atlas_2018 | brca_tcga_pan_can_atlas_2018_gistic |
| MAP2K4 | deep deletion | 46 | 2173 | 2.12% | brca_metabric | brca_metabric_cna |
| PTEN | deep deletion | 44 | 2173 | 2.02% | brca_metabric | brca_metabric_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) |
|---|---|---|
| ESR1 | 0.84–14.07% | brca_tcga_pan_can_atlas_2018: 9/1066 (0.84%) · brca_metabric: not assayed · brca_msk_2025: 65/462 (14.07%) |
| PGR | 0.66–3.5% | brca_tcga_pan_can_atlas_2018: 7/1066 (0.66%) · brca_metabric: not assayed · brca_msk_2025: 15/429 (3.5%) |
| ERBB2 | 2.81–10.39% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: 71/2433 (2.92%) · brca_msk_2025: 48/462 (10.39%) |
| PIK3CA | 32.46–59.96% | brca_tcga_pan_can_atlas_2018: 346/1066 (32.46%) · brca_metabric: 975/2433 (40.07%) · brca_msk_2025: 277/462 (59.96%) |
| AKT1 | 2.53–6.49% | brca_tcga_pan_can_atlas_2018: 27/1066 (2.53%) · brca_metabric: 98/2433 (4.03%) · brca_msk_2025: 30/462 (6.49%) |
| PTEN | 3.9–14.29% | brca_tcga_pan_can_atlas_2018: 58/1066 (5.44%) · brca_metabric: 95/2433 (3.9%) · brca_msk_2025: 66/462 (14.29%) |
| CDK4 | 0.0–1.08% | brca_tcga_pan_can_atlas_2018: 0/1066 (0.0%) · brca_metabric: not assayed · brca_msk_2025: 5/462 (1.08%) |
| CDK6 | 0.28–0.87% | brca_tcga_pan_can_atlas_2018: 3/1066 (0.28%) · brca_metabric: not assayed · brca_msk_2025: 4/462 (0.87%) |
| BRCA1 | 1.73–8.01% | brca_tcga_pan_can_atlas_2018: 27/1066 (2.53%) · brca_metabric: 42/2433 (1.73%) · brca_msk_2025: 37/462 (8.01%) |
| BRCA2 | 1.85–12.12% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: 45/2433 (1.85%) · brca_msk_2025: 56/462 (12.12%) |
| TP53 | 32.46–55.84% | brca_tcga_pan_can_atlas_2018: 346/1066 (32.46%) · brca_metabric: 861/2433 (35.39%) · brca_msk_2025: 258/462 (55.84%) |
| TACSTD2 | 0.0–0.0% | brca_tcga_pan_can_atlas_2018: 0/1066 (0.0%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| GATA3 | 10.97–13.64% | brca_tcga_pan_can_atlas_2018: 127/1066 (11.91%) · brca_metabric: 267/2433 (10.97%) · brca_msk_2025: 63/462 (13.64%) |
| CDH1 | 9.58–30.74% | brca_tcga_pan_can_atlas_2018: 127/1066 (11.91%) · brca_metabric: 233/2433 (9.58%) · brca_msk_2025: 142/462 (30.74%) |
| KMT2C | 9.1–27.92% | brca_tcga_pan_can_atlas_2018: 97/1066 (9.1%) · brca_metabric: 277/2433 (11.39%) · brca_msk_2025: 129/462 (27.92%) |
| MAP3K1 | 8.35–17.75% | brca_tcga_pan_can_atlas_2018: 89/1066 (8.35%) · brca_metabric: 236/2433 (9.7%) · brca_msk_2025: 82/462 (17.75%) |
| NCOR1 | 3.53–14.07% | brca_tcga_pan_can_atlas_2018: 50/1066 (4.69%) · brca_metabric: 86/2433 (3.53%) · brca_msk_2025: 65/462 (14.07%) |
| MAP2K4 | 3.25–7.79% | brca_tcga_pan_can_atlas_2018: 42/1066 (3.94%) · brca_metabric: 79/2433 (3.25%) · brca_msk_2025: 36/462 (7.79%) |
| RUNX1 | 3.33–5.41% | brca_tcga_pan_can_atlas_2018: 40/1066 (3.75%) · brca_metabric: 81/2433 (3.33%) · brca_msk_2025: 25/462 (5.41%) |
| ARID1A | 3.66–17.75% | brca_tcga_pan_can_atlas_2018: 39/1066 (3.66%) · brca_metabric: 114/2433 (4.69%) · brca_msk_2025: 82/462 (17.75%) |
| HUWE1 | 3.56–3.56% | brca_tcga_pan_can_atlas_2018: 38/1066 (3.56%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| NF1 | 3.47–20.56% | brca_tcga_pan_can_atlas_2018: 37/1066 (3.47%) · brca_metabric: 91/2433 (3.74%) · brca_msk_2025: 95/462 (20.56%) |
| CACNA1E | 3.47–3.47% | brca_tcga_pan_can_atlas_2018: 37/1066 (3.47%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| MDN1 | 3.38–3.38% | brca_tcga_pan_can_atlas_2018: 36/1066 (3.38%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| RELN | 3.19–3.19% | brca_tcga_pan_can_atlas_2018: 34/1066 (3.19%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| TBX3 | 3.1–13.2% | brca_tcga_pan_can_atlas_2018: 33/1066 (3.1%) · brca_metabric: 122/2433 (5.01%) · brca_msk_2025: 61/462 (13.2%) |
| MYCBP2 | 3.1–3.1% | brca_tcga_pan_can_atlas_2018: 33/1066 (3.1%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| SPEN | 3.0–15.8% | brca_tcga_pan_can_atlas_2018: 32/1066 (3.0%) · brca_metabric: not assayed · brca_msk_2025: 73/462 (15.8%) |
| KMT2D | 3.0–20.56% | brca_tcga_pan_can_atlas_2018: 32/1066 (3.0%) · brca_metabric: 176/2433 (7.23%) · brca_msk_2025: 95/462 (20.56%) |
| PRUNE2 | 2.91–2.91% | brca_tcga_pan_can_atlas_2018: 31/1066 (2.91%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| FOXA1 | 2.91–14.72% | brca_tcga_pan_can_atlas_2018: 31/1066 (2.91%) · brca_metabric: not assayed · brca_msk_2025: 68/462 (14.72%) |
| FAT1 | 2.91–16.88% | brca_tcga_pan_can_atlas_2018: 31/1066 (2.91%) · brca_metabric: not assayed · brca_msk_2025: 78/462 (16.88%) |
| VPS13C | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| TEX15 | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| MYH9 | 2.81–3.58% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: 87/2433 (3.58%) · brca_msk_2025: not assayed |
| MXRA5 | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| LYST | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| FCGBP | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| DYNC1H1 | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| BLTP1 | 2.81–2.81% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| AKAP9 | 2.81–5.88% | brca_tcga_pan_can_atlas_2018: 30/1066 (2.81%) · brca_metabric: 143/2433 (5.88%) · brca_msk_2025: not assayed |
| VPS13B | 2.72–2.72% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: not assayed · brca_msk_2025: not assayed |
| UTRN | 2.72–5.01% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: 122/2433 (5.01%) · brca_msk_2025: not assayed |
| PIK3R1 | 2.47–6.49% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: 60/2433 (2.47%) · brca_msk_2025: 30/462 (6.49%) |
| MED12 | 2.72–6.71% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: not assayed · brca_msk_2025: 31/462 (6.71%) |
| HERC2 | 2.72–6.45% | brca_tcga_pan_can_atlas_2018: 29/1066 (2.72%) · brca_metabric: 157/2433 (6.45%) · brca_msk_2025: not assayed |
| TG | 2.63–5.55% | brca_tcga_pan_can_atlas_2018: 28/1066 (2.63%) · brca_metabric: 135/2433 (5.55%) · brca_msk_2025: 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 2026-09-17; the page does not refresh source data at request time.
- Counts are patients with at least one non-silent call in the study's sequenced sample list; silent, intronic and UTR calls are excluded.
- For targeted-panel cohorts each gene divides by the patients whose panel carried it; a gene absent from the panel is shown as not assayed, not as zero.
- Copy-number rows use discrete calls (2 = high-level amplification, −2 = deep deletion) against the cohort's copy-number sample list, which is a different roster from the sequenced one.
- Cohorts are not pooled. Cross-study patient overlap has not been checked and no disease-wide frequency is reported.
- Structural variants and fusions are not read in this snapshot even where the study carries a profile; germline variants, mutational signatures, TMB and MSI are not reported.
- The gene set is the briefing's curated targets plus the reference cohort's most frequently mutated genes; it is not genome-wide.
How a machine should read this page
- Denominators: every frequency divides by the patients in one named cohort on whom the gene could be called; there is no disease-wide figure.
- Missing values:
not_assayed(the panel did not carry the gene),not_observed(assayed, none found) andnot_evaluable(the cohort could not be read) are three different facts and are never converted to zero. - Counting: patients, not samples; several samples from one patient count once. Non-silent calls only.
- Copy number: a separate assay with a separate roster; discrete calls at ±2 only.
- Hypermutation: flagged per cohort; the headline keeps all patients and the frequency without them is reported beside it.
- Provenance: every value carries the study id, the retrieval date and the processing version; the source is the cBioPortal public API.
Machine endpoints: full landscape · genes · cohorts · the disease's own facts: /disease/breast-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.