Disease intelligence · mutation landscape
Esophageal cancer mutation landscape
How often each gene is altered in esophageal 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 Esophageal Adenocarcinoma (TCGA, PanCancer Atlas) (182 sequenced patients, exome or genome), the most frequently altered of the 48 genes shown are TP53 86.81%, CDKN2A 39.01% (deep deletion), CCND1 34.62% (amplification), PIK3CA 17.58% (amplification), SOX2 16.48% (amplification). Each figure divides by the patients on whom that gene could be called.
2 of 182 patients are hypermutated (more than 1040 non-silent mutations, ten times the cohort median of 104); every gene's frequency without them is beside the headline.
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 | esca_tcga_pan_can_atlas_2018 182 pts · exome or genome | escc_ucla_2014 139 pts · mixed | egc_msk_2017 305 pts · targeted panel |
|---|---|---|---|
| TP53 SNV / small indel | 86.81%158/182 | 59.71%83/139 | 73.44%224/305 |
| ERBB2 SNV / small indel | 6.04%11/182 | 0% | 3.93%12/305 |
| ERBB2 amplification | 15.38%28/182 | · | 24.59%75/305 |
| CD274 SNV / small indel | 0% | 0% | 0% |
| CD274 amplification | 2.2%4/182 | · | 0.33%1/305 |
| CD274 deep deletion | 2.75%5/182 | · | 0.33%1/305 |
| PDCD1 SNV / small indel | 0.55%1/182 | 0% | 0.66%2/302 |
| PDCD1 deep deletion | 2.75%5/182 | · | 0.33%1/305 |
| CDKN2A SNV / small indel | 8.24%15/182 | 2.88%4/139 | 11.15%34/305 |
| CDKN2A deep deletion | 39.01%71/182 | · | 6.56%20/305 |
| NFE2L2 SNV / small indel | 9.89%18/182 | 5.76%8/139 | 0.66%2/305 |
| NFE2L2 amplification | 3.3%6/182 | · | 0% |
| SOX2 SNV / small indel | 0% | 0% | 0.33%1/305 |
| SOX2 amplification | 16.48%30/182 | · | 0% |
| EGFR SNV / small indel | 2.75%5/182 | 0.72%1/139 | 0.98%3/305 |
| EGFR amplification | 12.09%22/182 | · | 6.89%21/305 |
| CCND1 SNV / small indel | 0% | 0% | 0.33%1/305 |
| CCND1 amplification | 34.62%63/182 | · | 6.89%21/305 |
| KRAS SNV / small indel | 1.1%2/182 | 0% | 9.18%28/305 |
| KRAS amplification | 7.14%13/182 | · | 8.85%27/305 |
| SMAD4 SNV / small indel | 6.59%12/182 | 0% | 10.16%31/305 |
| SMAD4 deep deletion | 8.24%15/182 | · | 3.61%11/305 |
| CLDN18 SNV / small indel | 0.55%1/182 | 0% | · |
| CLDN18 amplification | 6.59%12/182 | · | 0% |
| KMT2D SNV / small indel | 11.54%21/182 | 17.99%25/139 | 8.85%27/305 |
| EYS SNV / small indel | 11.54%21/182 | 0% | · |
| EYS amplification | 2.2%4/182 | · | 0% |
| UNC13C SNV / small indel | 10.44%19/182 | 0% | · |
| PCDH15 SNV / small indel | 10.44%19/182 | 0% | · |
| DYNC2H1 SNV / small indel | 10.44%19/182 | 0% | · |
| DYNC2H1 amplification | 2.75%5/182 | · | 0% |
| PIK3CA SNV / small indel | 9.34%17/182 | 7.91%11/139 | 8.2%25/305 |
| PIK3CA amplification | 17.58%32/182 | · | 0% |
| LRRK2 SNV / small indel | 9.34%17/182 | 2.88%4/139 | · |
| LAMA1 SNV / small indel | 9.34%17/182 | 0% | · |
| DCDC1 SNV / small indel | 8.79%16/182 | 0% | · |
| DCDC1 amplification | 2.2%4/182 | · | 0% |
| NAV3 SNV / small indel | 8.24%15/182 | 5.04%7/139 | · |
| RIMS1 SNV / small indel | 7.69%14/182 | 0% | · |
| PTPRD SNV / small indel | 7.69%14/182 | 2.88%4/139 | 5.57%17/305 |
| PTPRD deep deletion | 6.04%11/182 | · | 0.98%3/305 |
| PRKDC SNV / small indel | 7.69%14/182 | 0% | · |
| NOTCH1 SNV / small indel | 7.69%14/182 | 7.91%11/139 | 4.92%15/305 |
| NOTCH1 amplification | 3.85%7/182 | · | 0.33%1/305 |
| IVL SNV / small indel | 7.69%14/182 | 0% | · |
| IVL amplification | 3.85%7/182 | · | 0% |
| HUWE1 SNV / small indel | 7.69%14/182 | 4.32%6/139 | · |
| HUWE1 deep deletion | 2.75%5/182 | · | 0% |
| FMN2 SNV / small indel | 7.69%14/182 | 3.6%5/139 | · |
| DCHS2 SNV / small indel | 7.69%14/182 | 0% | · |
| COL6A5 SNV / small indel | 7.69%14/182 | 0% | · |
| COL6A5 amplification | 3.85%7/182 | · | 0% |
| WDFY4 SNV / small indel | 7.14%13/182 | 0% | · |
| TRRAP SNV / small indel | 7.14%13/182 | 0% | · |
| TRRAP amplification | 10.99%20/182 | · | 0% |
| TENM4 SNV / small indel | 7.14%13/182 | 0% | · |
| TENM4 amplification | 3.3%6/182 | · | 0% |
| SI SNV / small indel | 7.14%13/182 | 6.47%9/139 | · |
| SI amplification | 15.93%29/182 | · | 0% |
| PREX2 SNV / small indel | 7.14%13/182 | 0% | 12.12%4/33 |
| PREX2 amplification | 2.75%5/182 | · | 0% |
| ERBB4 SNV / small indel | 7.14%13/182 | 4.32%6/139 | 8.2%25/305 |
| ERBB4 deep deletion | 2.75%5/182 | · | 0% |
| CDH11 SNV / small indel | 7.14%13/182 | 0% | 20.0%1/5 |
| ARID1A SNV / small indel | 7.14%13/182 | 1.44%2/139 | 13.77%42/305 |
| SMARCA4 SNV / small indel | 6.59%12/182 | 0.72%1/139 | 4.59%14/305 |
| PTPRT SNV / small indel | 6.59%12/182 | 0% | 7.54%23/305 |
| PTPRT amplification | 3.3%6/182 | · | 0.98%3/305 |
| PEG3 SNV / small indel | 6.59%12/182 | 0% | · |
| PDZD2 SNV / small indel | 6.59%12/182 | 2.88%4/139 | · |
| PDZD2 amplification | 7.69%14/182 | · | 0% |
| PCDH9 SNV / small indel | 6.59%12/182 | 3.6%5/139 | · |
| NBEA SNV / small indel | 6.59%12/182 | 4.32%6/139 | · |
| NBEA amplification | 3.85%7/182 | · | 0% |
| KMT2C SNV / small indel | 6.59%12/182 | 7.91%11/139 | 3.61%11/305 |
| KMT2C deep deletion | 2.2%4/182 | · | 0.33%1/305 |
| DOCK2 SNV / small indel | 6.59%12/182 | 0% | · |
| DCC SNV / small indel | 6.59%12/182 | 0% | · |
| DCC deep deletion | 4.4%8/182 | · | 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 158 of 182 patients in Esophageal Adenocarcinoma (TCGA, PanCancer Atlas).
CDKN2A is deleted in 71 of 182 patients in Esophageal Adenocarcinoma (TCGA, PanCancer Atlas).
CCND1 is amplified in 63 of 182 patients in Esophageal Adenocarcinoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
Headline values are from the reference cohort, esca_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 |
|---|---|---|---|---|---|---|---|---|
| TP53 | curated target | SNV / small indel | 158 / 182 | 86.81% | 87.78% | 3 / 3 | 59.71–86.81% | R175H (n=10), R248Q (n=9), R248W (n=6), R273H (n=6), R282W (n=5) |
| ERBB2 | curated target | amplification | 28 / 182 | 15.38% mutation 6.04% | 5.0% | 2 / 3 | 0.0–6.04% | V777L (n=2), S310F (n=2), A241V (n=1), M774dup (n=1), L662Q (n=1) |
| CD274 | curated target | deep deletion | 5 / 182 | 2.75% mutation 0.0% | 0.0% | 0 / 3 | 0.0–0.0% | none recurrent |
| PDCD1 | curated target | deep deletion | 5 / 182 | 2.75% mutation 0.55% | 0.0% | 2 / 3 | 0.0–0.66% | T36Hfs*70 (n=1) |
| CDKN2A | curated target | deep deletion | 71 / 182 | 39.01% mutation 8.24% | 7.78% | 3 / 3 | 2.88–11.15% | X153_splice (n=3), H83Y (n=2), G111Afs*8 (n=1), Y44* (n=1), P48L (n=1) |
| NFE2L2 | curated target | SNV / small indel | 18 / 182 | 9.89% | 10.0% | 3 / 3 | 0.66–9.89% | E79Q (n=2), Y46H (n=1), E79G (n=1), L30F (n=1), E79K (n=1) |
| SOX2 | curated target | amplification | 30 / 182 | 16.48% mutation 0.0% | 0.0% | 1 / 3 | 0.0–0.33% | none recurrent |
| EGFR | curated target | amplification | 22 / 182 | 12.09% mutation 2.75% | 2.22% | 3 / 3 | 0.72–2.75% | D314N (n=1), R574W (n=1), P373S (n=1), L1139F (n=1), G598E (n=1) |
| CCND1 | curated target | amplification | 63 / 182 | 34.62% mutation 0.0% | 0.0% | 1 / 3 | 0.0–0.33% | none recurrent |
| KRAS | curated target | amplification | 13 / 182 | 7.14% mutation 1.1% | 1.11% | 2 / 3 | 0.0–9.18% | G12D (n=2) |
| SMAD4 | curated target | deep deletion | 15 / 182 | 8.24% mutation 6.59% | 6.67% | 2 / 3 | 0.0–10.16% | R445* (n=2), R361H (n=1), R361C (n=1), W524L (n=1), G386V (n=1) |
| CLDN18 | curated target | amplification | 12 / 182 | 6.59% mutation 0.55% | 0.56% | 1 / 3 | 0.0–0.55% | Y66* (n=1) |
| KMT2D | by frequency | SNV / small indel | 21 / 182 | 11.54% | 11.11% | 3 / 3 | 8.85–17.99% | Q4732* (n=1), E4731D (n=1), R598H (n=1), Q4329* (n=1), Q3742* (n=1) |
| EYS | by frequency | SNV / small indel | 21 / 182 | 11.54% | 11.11% | 1 / 3 | 0.0–11.54% | F53V (n=1), K1519N (n=1), L1666F (n=1), E422A (n=1), I256K (n=1) |
| UNC13C | by frequency | SNV / small indel | 19 / 182 | 10.44% | 10.0% | 1 / 3 | 0.0–10.44% | L1614M (n=1), L1329V (n=1), K1905T (n=1), I1418V (n=1), A2023G (n=1) |
| PCDH15 | by frequency | SNV / small indel | 19 / 182 | 10.44% | 10.0% | 1 / 3 | 0.0–10.44% | P652H (n=2), L347P (n=1), K1508R (n=1), L347R (n=1), Q27H (n=1) |
| DYNC2H1 | by frequency | SNV / small indel | 19 / 182 | 10.44% | 10.0% | 1 / 3 | 0.0–10.44% | L3038R (n=1), L3066R (n=1), I1727T (n=1), K1870T (n=1), V3597I (n=1) |
| PIK3CA | by frequency | amplification | 32 / 182 | 17.58% mutation 9.34% | 9.44% | 3 / 3 | 7.91–9.34% | E545K (n=6), H1047L (n=3), E726K (n=2), K111N (n=1), F909C (n=1) |
| LRRK2 | by frequency | SNV / small indel | 17 / 182 | 9.34% | 8.89% | 2 / 3 | 2.88–9.34% | L325V (n=1), L744S (n=1), L2300F (n=1), E1156Q (n=1), L1776H (n=1) |
| LAMA1 | by frequency | SNV / small indel | 17 / 182 | 9.34% | 8.33% | 1 / 3 | 0.0–9.34% | R2772C (n=1), G1621S (n=1), N1253T (n=1), T1928P (n=1), V1269L (n=1) |
| DCDC1 | by frequency | SNV / small indel | 16 / 182 | 8.79% | 8.89% | 1 / 3 | 0.0–8.79% | Q85H (n=1), K292M (n=1), A282S (n=1), A731S (n=1), K347R (n=1) |
| NAV3 | by frequency | SNV / small indel | 15 / 182 | 8.24% | 7.78% | 2 / 3 | 5.04–8.24% | P251T (n=1), K558T (n=1), K1694N (n=1), V3L (n=1), L827P (n=1) |
| RIMS1 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.22% | 1 / 3 | 0.0–7.69% | W178R (n=1), K1437N (n=1), K1591R (n=1), K1590R (n=1), L1041R (n=1) |
| PTPRD | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.78% | 3 / 3 | 2.88–7.69% | R1674H (n=1), S363C (n=1), T820I (n=1), L840I (n=1), E675G (n=1) |
| PRKDC | by frequency | SNV / small indel | 14 / 182 | 7.69% | 6.67% | 1 / 3 | 0.0–7.69% | E2012K (n=1), E2009Q (n=1), L2509Ffs*4 (n=1), S3059F (n=1), X3798_splice (n=1) |
| NOTCH1 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.78% | 3 / 3 | 4.92–7.91% | A1696V (n=1), N927Qfs*17 (n=1), E488K (n=1), N304Mfs*327 (n=1), X1723_splice (n=1) |
| IVL | by frequency | SNV / small indel | 14 / 182 | 7.69% | 6.67% | 1 / 3 | 0.0–7.69% | E180G (n=1), Q439H (n=1), L173P (n=1), Q272H (n=1), Q339R (n=1) |
| HUWE1 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 6.67% | 2 / 3 | 4.32–7.69% | M4213I (n=1), D3987N (n=1), P715T (n=1), E3184K (n=1), D768E (n=1) |
| FMN2 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.22% | 2 / 3 | 3.6–7.69% | L1682R (n=1), Q1400R (n=1), Q745Rfs*11 (n=1), G1005R (n=1), S11R (n=1) |
| DCHS2 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.22% | 1 / 3 | 0.0–7.69% | L612R (n=1), V423I (n=1), S62Y (n=1), K2097Q (n=1), D503N (n=1) |
| COL6A5 | by frequency | SNV / small indel | 14 / 182 | 7.69% | 7.22% | 1 / 3 | 0.0–7.69% | H1000N (n=1), T2472P (n=1), G337R (n=1), R2471* (n=1), W2392C (n=1) |
| WDFY4 | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.67% | 1 / 3 | 0.0–7.14% | F2041L (n=1), K320I (n=1), R3111Q (n=1), L718P (n=1), L2962H (n=1) |
| TRRAP | by frequency | amplification | 20 / 182 | 10.99% mutation 7.14% | 6.67% | 1 / 3 | 0.0–7.14% | E3477K (n=1), W3444C (n=1), A1923V (n=1), T654M (n=1), R2917C (n=1) |
| TENM4 | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.67% | 1 / 3 | 0.0–7.14% | R2662S (n=1), D1805N (n=1), R1832Q (n=1), R1371C (n=1), R1018H (n=1) |
| SI | by frequency | amplification | 29 / 182 | 15.93% mutation 7.14% | 7.22% | 2 / 3 | 6.47–7.14% | L1167V (n=1), G676Wfs*8 (n=1), G1199C (n=1), V1450G (n=1), F1616I (n=1) |
| PREX2 | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.67% | 2 / 3 | 0.0–12.12% | N137Tfs*3 (n=1), V416L (n=1), E127G (n=1), R281W (n=1), L50V (n=1) |
| ERBB4 | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.11% | 3 / 3 | 4.32–8.2% | S449Y (n=1), S430R (n=1), E928* (n=1), C293Y (n=1), N1305Ifs*57 (n=1) |
| CDH11 | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.67% | 2 / 3 | 0.0–20.0% | F488V (n=1), T219S (n=1), A551T (n=1), D596N (n=1), F358V (n=1) |
| ARID1A | by frequency | SNV / small indel | 13 / 182 | 7.14% | 6.67% | 3 / 3 | 1.44–13.77% | Y560* (n=1), Q1346* (n=1), N791K (n=1), G2087R (n=1), W1073Mfs*32 (n=1) |
| SMARCA4 | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.11% | 3 / 3 | 0.72–6.59% | T910M (n=2), R874H (n=1), E1211A (n=1), G235D (n=1), R966W (n=1) |
| PTPRT | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.11% | 2 / 3 | 0.0–7.54% | L668V (n=2), F664C (n=1), S647P (n=1), R359P (n=1), G411S (n=1) |
| PEG3 | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.11% | 1 / 3 | 0.0–6.59% | A1395S (n=1), L1010V (n=1), V1413A (n=1), G1338V (n=1), E1398D (n=1) |
| PDZD2 | by frequency | amplification | 14 / 182 | 7.69% mutation 6.59% | 6.67% | 2 / 3 | 2.88–6.59% | A162D (n=1), V2477M (n=1), T1060A (n=1), L2671F (n=1), T1425A (n=1) |
| PCDH9 | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.11% | 2 / 3 | 3.6–6.59% | F1161C (n=1), E36D (n=1), E1072G (n=1), E699K (n=1), S905G (n=1) |
| NBEA | by frequency | SNV / small indel | 12 / 182 | 6.59% | 5.56% | 2 / 3 | 4.32–6.59% | L1537P (n=1), L1914R (n=1), T2103M (n=1), R1552Q (n=1), E156D (n=1) |
| KMT2C | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.67% | 3 / 3 | 3.61–7.91% | D4635V (n=1), T2078A (n=1), D3628N (n=1), M1607Kfs*59 (n=1), G972E (n=1) |
| DOCK2 | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.11% | 1 / 3 | 0.0–6.59% | P60R (n=1), K1801R (n=1), K1006T (n=1), K1058T (n=1), R228K (n=1) |
| DCC | by frequency | SNV / small indel | 12 / 182 | 6.59% | 6.67% | 1 / 3 | 0.0–6.59% | R1343H (n=1), N294T (n=1), Q410H (n=1), M915V (n=1), R884W (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 |
|---|---|---|---|---|---|---|---|---|---|
| Esophageal Adenocarcinoma (TCGA, PanCancer Atlas) reference | esca_tcga_pan_can_atlas_2018 | 182 observed | 182 / 182 | exome or genome | WES (182) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 2 | 104.0 |
| Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014) | escc_ucla_2014 | 139 observed | 139 / 139 | mixed | UCLA_1202 (119), WES (20) | hg19 | SNV, small indel | 0 | 15 |
| Metastatic Esophagogastric Cancer (MSK, Cancer Discovery 2017) | egc_msk_2017 | 305 observed | 341 / 341 | targeted panel | IMPACT410 (178), IMPACT341 (127), IMPACT468 (28), IMPACT300 (8) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 5 |
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 | 71 | 182 | 39.01% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| CCND1 | amplification | 63 | 182 | 34.62% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| ERBB2 | amplification | 75 | 305 | 24.59% | egc_msk_2017 | egc_msk_2017_cna |
| PIK3CA | amplification | 32 | 182 | 17.58% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| SOX2 | amplification | 30 | 182 | 16.48% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| SI | amplification | 29 | 182 | 15.93% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| ERBB2 | amplification | 28 | 182 | 15.38% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| EGFR | amplification | 22 | 182 | 12.09% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| TRRAP | amplification | 20 | 182 | 10.99% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| KRAS | amplification | 27 | 305 | 8.85% | egc_msk_2017 | egc_msk_2017_cna |
| SMAD4 | deep deletion | 15 | 182 | 8.24% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| PDZD2 | amplification | 14 | 182 | 7.69% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| KRAS | amplification | 13 | 182 | 7.14% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| EGFR | amplification | 21 | 305 | 6.89% | egc_msk_2017 | egc_msk_2017_cna |
| CCND1 | amplification | 21 | 305 | 6.89% | egc_msk_2017 | egc_msk_2017_cna |
| CLDN18 | amplification | 12 | 182 | 6.59% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| CDKN2A | deep deletion | 20 | 305 | 6.56% | egc_msk_2017 | egc_msk_2017_cna |
| PTPRD | deep deletion | 11 | 182 | 6.04% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| DCC | deep deletion | 8 | 182 | 4.4% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| NOTCH1 | amplification | 7 | 182 | 3.85% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| IVL | amplification | 7 | 182 | 3.85% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| COL6A5 | amplification | 7 | 182 | 3.85% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| NBEA | amplification | 7 | 182 | 3.85% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| SMAD4 | deep deletion | 11 | 305 | 3.61% | egc_msk_2017 | egc_msk_2017_cna |
| NFE2L2 | amplification | 6 | 182 | 3.3% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| TENM4 | amplification | 6 | 182 | 3.3% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| PTPRT | amplification | 6 | 182 | 3.3% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| CD274 | deep deletion | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| PDCD1 | deep deletion | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| DYNC2H1 | amplification | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| HUWE1 | deep deletion | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| PREX2 | amplification | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| ERBB4 | deep deletion | 5 | 182 | 2.75% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| CD274 | amplification | 4 | 182 | 2.2% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| EYS | amplification | 4 | 182 | 2.2% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| DCDC1 | amplification | 4 | 182 | 2.2% | esca_tcga_pan_can_atlas_2018 | esca_tcga_pan_can_atlas_2018_gistic |
| KMT2C | deep deletion | 4 | 182 | 2.2% | esca_tcga_pan_can_atlas_2018 | esca_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) |
|---|---|---|
| TP53 | 59.71–86.81% | esca_tcga_pan_can_atlas_2018: 158/182 (86.81%) · escc_ucla_2014: 83/139 (59.71%) · egc_msk_2017: 224/305 (73.44%) |
| ERBB2 | 0.0–6.04% | esca_tcga_pan_can_atlas_2018: 11/182 (6.04%) · escc_ucla_2014: 0/139 (0.0%) · egc_msk_2017: 12/305 (3.93%) |
| CD274 | 0.0–0.0% | esca_tcga_pan_can_atlas_2018: 0/182 (0.0%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 0/302 (0.0%) |
| PDCD1 | 0.0–0.66% | esca_tcga_pan_can_atlas_2018: 1/182 (0.55%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 2/302 (0.66%) |
| CDKN2A | 2.88–11.15% | esca_tcga_pan_can_atlas_2018: 15/182 (8.24%) · escc_ucla_2014: 4/139 (2.88%) · egc_msk_2017: 34/305 (11.15%) |
| NFE2L2 | 0.66–9.89% | esca_tcga_pan_can_atlas_2018: 18/182 (9.89%) · escc_ucla_2014: 8/139 (5.76%) · egc_msk_2017: 2/305 (0.66%) |
| SOX2 | 0.0–0.33% | esca_tcga_pan_can_atlas_2018: 0/182 (0.0%) · escc_ucla_2014: 0/139 (0.0%) · egc_msk_2017: 1/305 (0.33%) |
| EGFR | 0.72–2.75% | esca_tcga_pan_can_atlas_2018: 5/182 (2.75%) · escc_ucla_2014: 1/139 (0.72%) · egc_msk_2017: 3/305 (0.98%) |
| CCND1 | 0.0–0.33% | esca_tcga_pan_can_atlas_2018: 0/182 (0.0%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 1/305 (0.33%) |
| KRAS | 0.0–9.18% | esca_tcga_pan_can_atlas_2018: 2/182 (1.1%) · escc_ucla_2014: 0/139 (0.0%) · egc_msk_2017: 28/305 (9.18%) |
| SMAD4 | 0.0–10.16% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 0/139 (0.0%) · egc_msk_2017: 31/305 (10.16%) |
| CLDN18 | 0.0–0.55% | esca_tcga_pan_can_atlas_2018: 1/182 (0.55%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| KMT2D | 8.85–17.99% | esca_tcga_pan_can_atlas_2018: 21/182 (11.54%) · escc_ucla_2014: 25/139 (17.99%) · egc_msk_2017: 27/305 (8.85%) |
| EYS | 0.0–11.54% | esca_tcga_pan_can_atlas_2018: 21/182 (11.54%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| UNC13C | 0.0–10.44% | esca_tcga_pan_can_atlas_2018: 19/182 (10.44%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| PCDH15 | 0.0–10.44% | esca_tcga_pan_can_atlas_2018: 19/182 (10.44%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| DYNC2H1 | 0.0–10.44% | esca_tcga_pan_can_atlas_2018: 19/182 (10.44%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| PIK3CA | 7.91–9.34% | esca_tcga_pan_can_atlas_2018: 17/182 (9.34%) · escc_ucla_2014: 11/139 (7.91%) · egc_msk_2017: 25/305 (8.2%) |
| LRRK2 | 2.88–9.34% | esca_tcga_pan_can_atlas_2018: 17/182 (9.34%) · escc_ucla_2014: 4/139 (2.88%) · egc_msk_2017: not assayed |
| LAMA1 | 0.0–9.34% | esca_tcga_pan_can_atlas_2018: 17/182 (9.34%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| DCDC1 | 0.0–8.79% | esca_tcga_pan_can_atlas_2018: 16/182 (8.79%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| NAV3 | 5.04–8.24% | esca_tcga_pan_can_atlas_2018: 15/182 (8.24%) · escc_ucla_2014: 7/139 (5.04%) · egc_msk_2017: not assayed |
| RIMS1 | 0.0–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| PTPRD | 2.88–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 4/139 (2.88%) · egc_msk_2017: 17/305 (5.57%) |
| PRKDC | 0.0–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| NOTCH1 | 4.92–7.91% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 11/139 (7.91%) · egc_msk_2017: 15/305 (4.92%) |
| IVL | 0.0–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| HUWE1 | 4.32–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 6/139 (4.32%) · egc_msk_2017: not assayed |
| FMN2 | 3.6–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 5/139 (3.6%) · egc_msk_2017: not assayed |
| DCHS2 | 0.0–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| COL6A5 | 0.0–7.69% | esca_tcga_pan_can_atlas_2018: 14/182 (7.69%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| WDFY4 | 0.0–7.14% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| TRRAP | 0.0–7.14% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| TENM4 | 0.0–7.14% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| SI | 6.47–7.14% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 9/139 (6.47%) · egc_msk_2017: not assayed |
| PREX2 | 0.0–12.12% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 4/33 (12.12%) |
| ERBB4 | 4.32–8.2% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 6/139 (4.32%) · egc_msk_2017: 25/305 (8.2%) |
| CDH11 | 0.0–20.0% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 1/5 (20.0%) |
| ARID1A | 1.44–13.77% | esca_tcga_pan_can_atlas_2018: 13/182 (7.14%) · escc_ucla_2014: 2/139 (1.44%) · egc_msk_2017: 42/305 (13.77%) |
| SMARCA4 | 0.72–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 1/139 (0.72%) · egc_msk_2017: 14/305 (4.59%) |
| PTPRT | 0.0–7.54% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 23/305 (7.54%) |
| PEG3 | 0.0–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| PDZD2 | 2.88–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 4/139 (2.88%) · egc_msk_2017: not assayed |
| PCDH9 | 3.6–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 5/139 (3.6%) · egc_msk_2017: not assayed |
| NBEA | 4.32–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 6/139 (4.32%) · egc_msk_2017: not assayed |
| KMT2C | 3.61–7.91% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 11/139 (7.91%) · egc_msk_2017: 11/305 (3.61%) |
| DOCK2 | 0.0–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: not assayed |
| DCC | 0.0–6.59% | esca_tcga_pan_can_atlas_2018: 12/182 (6.59%) · escc_ucla_2014: 0/20 (0.0%) · egc_msk_2017: 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/esophageal-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.