Disease intelligence · mutation landscape
Soft tissue sarcoma mutation landscape
How often each gene is altered in soft tissue sarcoma, 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 Sarcoma (TCGA, PanCancer Atlas) (255 sequenced patients, exome or genome), the most frequently altered of the 49 genes shown are TP53 33.33%, MDM2 18.58% (amplification), CDK4 17.39% (amplification), RB1 14.62% (deep deletion), ATRX 14.12%. Each figure divides by the patients on whom that gene could be called.
8 of 255 patients are hypermutated (more than 380 non-silent mutations, ten times the cohort median of 38); 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 (ALK, PDGFRB, SS18, CTAG1B): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.
2 cohorts are shown and none are pooled; overlap between them has not been checked and there is no disease-wide percentage.
Evidence boundary: frequency here is a count in a named cohort. Whether an alteration is a driver, is actionable, or has a drug is the briefing's question and is not inferred from these numbers.
What is altered, by cohort
One row per alteration, not per gene: a gene that is amplified and rarely mutated (ERBB2, MYCN, EGFR) gets a row for each. Every cell divides by its own denominator — the patients in that cohort on whom that gene could be called. Copy-number rows are shown only where at least one cohort reaches 2%.
| Alteration | sarc_tcga_pan_can_atlas_2018 255 pts · exome or genome | sarcoma_mskcc_2022 2138 pts · targeted panel |
|---|---|---|
| TP53 SNV / small indel | 33.33%85/255 | 18.57%397/2138 |
| TP53 deep deletion | 9.88%25/253 | 5.24%112/2138 |
| MDM2 SNV / small indel | 1.96%5/255 | 0.28%6/2138 |
| MDM2 amplification | 18.58%47/253 | 12.16%260/2138 |
| CDK4 SNV / small indel | 0.39%1/255 | 0.23%5/2138 |
| CDK4 amplification | 17.39%44/253 | 11.51%246/2138 |
| RB1 SNV / small indel | 9.8%25/255 | 4.63%99/2138 |
| RB1 deep deletion | 14.62%37/253 | 7.16%153/2138 |
| PDGFRA SNV / small indel | 0.39%1/255 | 2.06%44/2138 |
| PDGFRA amplification | 3.16%8/253 | 2.06%44/2138 |
| NTRK1 SNV / small indel | 1.18%3/255 | 0.47%10/2138 |
| NTRK1 amplification | 4.35%11/253 | 1.5%32/2138 |
| ALK SNV / small indel | 1.18%3/255 | 0.7%15/2138 |
| PDGFRB SNV / small indel | 1.18%3/255 | 0.8%17/2138 |
| NF1 SNV / small indel | 3.92%10/255 | 3.04%65/2138 |
| NF1 deep deletion | 3.95%10/253 | 1.22%26/2138 |
| SS18 SNV / small indel | 0% | · |
| TERT SNV / small indel | 1.57%4/255 | 0.56%12/2138 |
| TERT amplification | 4.74%12/253 | 3.51%75/2138 |
| CTAG1B SNV / small indel | 0% | · |
| ATRX SNV / small indel | 14.12%36/255 | 6.83%146/2138 |
| ATRX deep deletion | 6.72%17/253 | 1.82%39/2138 |
| SCN2A SNV / small indel | 5.1%13/255 | · |
| FCGBP SNV / small indel | 4.31%11/255 | · |
| FCGBP amplification | 3.95%10/253 | 0% |
| SPHKAP SNV / small indel | 3.92%10/255 | · |
| SPHKAP deep deletion | 4.35%11/253 | 0% |
| PRKDC SNV / small indel | 3.92%10/255 | · |
| NAV3 SNV / small indel | 3.92%10/255 | · |
| NAV3 amplification | 10.67%27/253 | 0% |
| FREM2 SNV / small indel | 3.92%10/255 | · |
| FREM2 deep deletion | 2.37%6/253 | 0% |
| DOCK3 SNV / small indel | 3.92%10/255 | · |
| CFAP54 SNV / small indel | 3.92%10/255 | · |
| ZAN SNV / small indel | 3.53%9/255 | · |
| TRPM6 SNV / small indel | 3.53%9/255 | · |
| TRPM6 amplification | 2.37%6/253 | 0% |
| SPTBN4 SNV / small indel | 3.53%9/255 | · |
| SPTBN4 amplification | 3.56%9/253 | 0% |
| MYO15A SNV / small indel | 3.53%9/255 | · |
| MYO15A amplification | 9.49%24/253 | 0% |
| MGAM SNV / small indel | 3.53%9/255 | · |
| KMT2D SNV / small indel | 3.53%9/255 | 2.53%54/2138 |
| FRAS1 SNV / small indel | 3.53%9/255 | · |
| DOCK2 SNV / small indel | 3.53%9/255 | · |
| DOCK2 amplification | 2.37%6/253 | 0% |
| DISP3 SNV / small indel | 3.53%9/255 | · |
| DISP3 amplification | 2.37%6/253 | 0% |
| DCHS2 SNV / small indel | 3.53%9/255 | · |
| WDR87 SNV / small indel | 3.14%8/255 | · |
| UNC80 SNV / small indel | 3.14%8/255 | · |
| UNC13C SNV / small indel | 3.14%8/255 | · |
| TNRC18 SNV / small indel | 3.14%8/255 | · |
| TNRC18 amplification | 2.77%7/253 | 0% |
| TMEM132C SNV / small indel | 3.14%8/255 | · |
| TMEM132C amplification | 2.37%6/253 | 0% |
| SHANK2 SNV / small indel | 3.14%8/255 | · |
| SCN9A SNV / small indel | 3.14%8/255 | · |
| RELN SNV / small indel | 3.14%8/255 | · |
| PKHD1 SNV / small indel | 3.14%8/255 | · |
| PKHD1 amplification | 2.37%6/253 | 0% |
| PEG3 SNV / small indel | 3.14%8/255 | · |
| NRXN1 SNV / small indel | 3.14%8/255 | · |
| MYH7 SNV / small indel | 3.14%8/255 | · |
| MAP1A SNV / small indel | 3.14%8/255 | · |
| LRP1 SNV / small indel | 3.14%8/255 | · |
| LRP1 amplification | 4.35%11/253 | 0% |
| KIAA1549 SNV / small indel | 3.14%8/255 | · |
| KCNH8 SNV / small indel | 3.14%8/255 | · |
| KALRN SNV / small indel | 3.14%8/255 | · |
| FAT1 SNV / small indel | 3.14%8/255 | 1.82%39/2138 |
| FAT1 deep deletion | 2.77%7/253 | 0.75%16/2138 |
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 85 of 255 patients in Sarcoma (TCGA, PanCancer Atlas).
MDM2 is amplified in 47 of 253 patients in Sarcoma (TCGA, PanCancer Atlas).
CDK4 is amplified in 44 of 253 patients in Sarcoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
Headline values are from the reference cohort, sarc_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 | 85 / 255 | 33.33% | 32.39% | 2 / 2 | 18.57–33.33% | X187_splice (n=4), R175H (n=4), R248W (n=3), W91* (n=2), C275Y (n=2) |
| MDM2 | curated target | amplification | 47 / 253 | 18.58% mutation 1.96% | 1.62% | 2 / 2 | 0.28–1.96% | L230F (n=1), S221C (n=1), I211T (n=1), D231N (n=1), V234I (n=1) |
| CDK4 | curated target | amplification | 44 / 253 | 17.39% mutation 0.39% | 0.4% | 2 / 2 | 0.23–0.39% | G15R (n=1) |
| RB1 | curated target | deep deletion | 37 / 253 | 14.62% mutation 9.8% | 8.91% | 2 / 2 | 4.63–9.8% | Q384* (n=1), Q504* (n=1), Y155* (n=1), X888_splice (n=1), N623Kfs*30 (n=1) |
| PDGFRA | curated target | amplification | 8 / 253 | 3.16% mutation 0.39% | 0.0% | 2 / 2 | 0.39–2.06% | M448R (n=1) |
| NTRK1 | curated target | amplification | 11 / 253 | 4.35% mutation 1.18% | 0.81% | 2 / 2 | 0.47–1.18% | V354I (n=1), G169R (n=1), R583C (n=1) |
| ALK | curated target | SNV / small indel | 3 / 255 | 1.18% | 0.81% | 2 / 2 | 0.7–1.18% | X786_splice (n=1), E570D (n=1), L1319I (n=1) |
| PDGFRB | curated target | amplification | 3 / 253 | 1.19% mutation 1.18% | 0.4% | 2 / 2 | 0.8–1.18% | P346T (n=1), D850Y (n=1), L1076F (n=1) |
| NF1 | curated target | deep deletion | 10 / 253 | 3.95% mutation 3.92% | 3.24% | 2 / 2 | 3.04–3.92% | Y628Tfs*3 (n=1), H1170Q (n=1), L1564F (n=1), X2215_splice (n=1), A308Cfs*7 (n=1) |
| SS18 | curated target | amplification | 3 / 253 | 1.19% mutation 0.0% | 0.0% | 0 / 2 | 0.0–0.0% | none recurrent |
| TERT | curated target | amplification | 12 / 253 | 4.74% mutation 1.57% | 1.21% | 2 / 2 | 0.56–1.57% | R698W (n=1), L621I (n=1), N1120S (n=1), G1060C (n=1) |
| CTAG1B | curated target | SNV / small indel | 0 / 255 | 0.0% | 0.0% | 0 / 2 | 0.0–0.0% | none recurrent |
| ATRX | by frequency | SNV / small indel | 36 / 255 | 14.12% | 14.57% | 2 / 2 | 6.83–14.12% | M828* (n=1), G1567D (n=1), S1253* (n=1), G1589E (n=1), E723* (n=1) |
| SCN2A | by frequency | SNV / small indel | 13 / 255 | 5.1% | 5.26% | 1 / 2 | 5.1–5.1% | R379C (n=1), G1149* (n=1), F1677Y (n=1), K749E (n=1), V1579M (n=1) |
| FCGBP | by frequency | SNV / small indel | 11 / 255 | 4.31% | 3.64% | 1 / 2 | 4.31–4.31% | X2334_splice (n=1), G877S (n=1), K4889Q (n=1), A407D (n=1), G1220S (n=1) |
| SPHKAP | by frequency | deep deletion | 11 / 253 | 4.35% mutation 3.92% | 3.64% | 1 / 2 | 3.92–3.92% | S1397I (n=1), E578Rfs*2 (n=1), T827K (n=1), E594K (n=1), E578G (n=1) |
| PRKDC | by frequency | SNV / small indel | 10 / 255 | 3.92% | 3.24% | 1 / 2 | 3.92–3.92% | Q3073* (n=1), G2708E (n=1), L1857I (n=1), A1148E (n=1), A1404D (n=1) |
| NAV3 | by frequency | amplification | 27 / 253 | 10.67% mutation 3.92% | 2.83% | 1 / 2 | 3.92–3.92% | S1292L (n=1), S1081N (n=1), S1293Y (n=1), A1620S (n=1), R750Q (n=1) |
| FREM2 | by frequency | SNV / small indel | 10 / 255 | 3.92% | 3.24% | 1 / 2 | 3.92–3.92% | M1204L (n=1), L763F (n=1), M1193I (n=1), X2057_splice (n=1), T2812N (n=1) |
| DOCK3 | by frequency | SNV / small indel | 10 / 255 | 3.92% | 1.62% | 1 / 2 | 3.92–3.92% | R844L (n=1), E893V (n=1), M1622I (n=1), A1318S (n=1), E753K (n=1) |
| CFAP54 | by frequency | SNV / small indel | 10 / 255 | 3.92% | 2.83% | 1 / 2 | 3.92–3.92% | W1941S (n=1), I1616S (n=1), X190_splice (n=1), D782N (n=1), K173T (n=1) |
| ZAN | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.02% | 1 / 2 | 3.53–3.53% | L1614P (n=1), Q1704H (n=1), A2118S (n=1), E932G (n=1), Q1772H (n=1) |
| TRPM6 | by frequency | SNV / small indel | 9 / 255 | 3.53% | 3.24% | 1 / 2 | 3.53–3.53% | I513F (n=1), S1790Y (n=1), S90R (n=1), K1492N (n=1), D309V (n=1) |
| SPTBN4 | by frequency | amplification | 9 / 253 | 3.56% mutation 3.53% | 2.02% | 1 / 2 | 3.53–3.53% | A2T (n=1), S378N (n=1), A1001T (n=1), K1970N (n=1), E868K (n=1) |
| MYO15A | by frequency | amplification | 24 / 253 | 9.49% mutation 3.53% | 2.83% | 1 / 2 | 3.53–3.53% | L358I (n=1), D1454Y (n=1), R567L (n=1), V378I (n=1), R1926C (n=1) |
| MGAM | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.83% | 1 / 2 | 3.53–3.53% | K475E (n=1), D311Y (n=1), T1204A (n=1), G1548V (n=1), P106L (n=1) |
| KMT2D | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.43% | 2 / 2 | 2.53–3.53% | P3375T (n=1), F4819L (n=1), W5395R (n=1), P457L (n=1), E4061K (n=1) |
| FRAS1 | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.43% | 1 / 2 | 3.53–3.53% | X1571_splice (n=1), P2848L (n=1), S147I (n=1), C973F (n=1), X3260_splice (n=1) |
| DOCK2 | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.83% | 1 / 2 | 3.53–3.53% | T1504M (n=1), E821Sfs*9 (n=1), G1403V (n=1), V1262I (n=1), Y1029N (n=1) |
| DISP3 | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.43% | 1 / 2 | 3.53–3.53% | V1294I (n=1), K913N (n=1), S1145I (n=1), R901H (n=1), V1253I (n=1) |
| DCHS2 | by frequency | SNV / small indel | 9 / 255 | 3.53% | 2.83% | 1 / 2 | 3.53–3.53% | D1143N (n=1), P2002S (n=1), F634L (n=1), S95F (n=1), N1510S (n=1) |
| WDR87 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.02% | 1 / 2 | 3.14–3.14% | R1098W (n=1), E1656K (n=1), L861F (n=1), M1357L (n=1), E2030K (n=1) |
| UNC80 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 1.62% | 1 / 2 | 3.14–3.14% | V189M (n=1), S1489I (n=1), A2988S (n=1), K1671E (n=1), T399A (n=1) |
| UNC13C | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.83% | 1 / 2 | 3.14–3.14% | T1107I (n=1), K345E (n=1), E1349* (n=1), L1568V (n=1), Q2045* (n=1) |
| TNRC18 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.02% | 1 / 2 | 3.14–3.14% | A1478V (n=1), A2697V (n=1), R2383* (n=1), R721L (n=1), E1736K (n=1) |
| TMEM132C | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | A443T (n=1), T86I (n=1), M385I (n=1), E910K (n=1), R703W (n=1) |
| SHANK2 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | A998V (n=1), G1213V (n=1), L283I (n=1), V695I (n=1), R829W (n=1) |
| SCN9A | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | A438P (n=1), S849F (n=1), L1395I (n=1), K1059E (n=1), F879L (n=1) |
| RELN | by frequency | SNV / small indel | 8 / 255 | 3.14% | 1.21% | 1 / 2 | 3.14–3.14% | L3154I (n=1), D2171V (n=1), R2216* (n=1), R2457C (n=1), S3275F (n=1) |
| PKHD1 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 3.24% | 1 / 2 | 3.14–3.14% | N2300S (n=1), R3620C (n=1), I1192F (n=1), V2429I (n=1), P3221L (n=1) |
| PEG3 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.83% | 1 / 2 | 3.14–3.14% | R148I (n=1), L254M (n=1), K66E (n=1), P4L (n=1), V951L (n=1) |
| NRXN1 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.83% | 1 / 2 | 3.14–3.14% | R121H (n=1), P619T (n=1), L1352F (n=1), L296W (n=1), H526P (n=1) |
| MYH7 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.83% | 1 / 2 | 3.14–3.14% | Y386* (n=1), E1743del (n=1), D685E (n=1), I1238S (n=1), R1818W (n=1) |
| MAP1A | by frequency | SNV / small indel | 8 / 255 | 3.14% | 1.62% | 1 / 2 | 3.14–3.14% | A640V (n=1), E439D (n=1), S1749I (n=1), R1657I (n=1), L2247Q (n=1) |
| LRP1 | by frequency | amplification | 11 / 253 | 4.35% mutation 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | D1464Y (n=1), S1290I (n=1), I2618M (n=1), W3351* (n=1), D2819N (n=1) |
| KIAA1549 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | V1007I (n=1), A732V (n=1), X1410_splice (n=1), V595F (n=1), E882K (n=1) |
| KCNH8 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.43% | 1 / 2 | 3.14–3.14% | A587V (n=1), D992H (n=1), M603I (n=1), R835Q (n=1), A555S (n=1) |
| KALRN | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.02% | 1 / 2 | 3.14–3.14% | E41K (n=1), R1494W (n=1), R1071W (n=1), A1093D (n=1), V278E (n=1) |
| FAT1 | by frequency | SNV / small indel | 8 / 255 | 3.14% | 2.83% | 2 / 2 | 1.82–3.14% | E2498V (n=1), E2705* (n=1), D177N (n=1), L3599V (n=1), Q3572* (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 |
|---|---|---|---|---|---|---|---|---|---|
| Sarcoma (TCGA, PanCancer Atlas) reference | sarc_tcga_pan_can_atlas_2018 | 255 observed | 255 / 255 | exome or genome | WES (255) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 8 | 38 |
| Sarcoma (MSK, Nat Commun. 2022) | sarcoma_mskcc_2022 | 2138 observed | 2138 / 2138 | targeted panel | IMPACT468 (1356), IMPACT410 (573), IMPACT341 (209) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 1 | 1.0 |
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 |
|---|---|---|---|---|---|---|
| MDM2 | amplification | 47 | 253 | 18.58% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| CDK4 | amplification | 44 | 253 | 17.39% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 37 | 253 | 14.62% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| MDM2 | amplification | 260 | 2138 | 12.16% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
| CDK4 | amplification | 246 | 2138 | 11.51% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
| NAV3 | amplification | 27 | 253 | 10.67% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TP53 | deep deletion | 25 | 253 | 9.88% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| MYO15A | amplification | 24 | 253 | 9.49% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| RB1 | deep deletion | 153 | 2138 | 7.16% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
| ATRX | deep deletion | 17 | 253 | 6.72% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TP53 | deep deletion | 112 | 2138 | 5.24% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
| TERT | amplification | 12 | 253 | 4.74% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| NTRK1 | amplification | 11 | 253 | 4.35% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| SPHKAP | deep deletion | 11 | 253 | 4.35% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| LRP1 | amplification | 11 | 253 | 4.35% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| NF1 | deep deletion | 10 | 253 | 3.95% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| FCGBP | amplification | 10 | 253 | 3.95% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| SPTBN4 | amplification | 9 | 253 | 3.56% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TERT | amplification | 75 | 2138 | 3.51% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
| PDGFRA | amplification | 8 | 253 | 3.16% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TNRC18 | amplification | 7 | 253 | 2.77% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| FAT1 | deep deletion | 7 | 253 | 2.77% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| FREM2 | deep deletion | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TRPM6 | amplification | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| DOCK2 | amplification | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| DISP3 | amplification | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| TMEM132C | amplification | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| PKHD1 | amplification | 6 | 253 | 2.37% | sarc_tcga_pan_can_atlas_2018 | sarc_tcga_pan_can_atlas_2018_gistic |
| PDGFRA | amplification | 44 | 2138 | 2.06% | sarcoma_mskcc_2022 | sarcoma_mskcc_2022_cna |
Cohort-aware frequencies
Each row is calculated from unique patients in that study's sequenced sample list. The range is descriptive; no pooled estimate is shown because cross-study overlap and assay comparability have not been checked.
| Gene | Range | Per cohort (altered / tested) |
|---|---|---|
| TP53 | 18.57–33.33% | sarc_tcga_pan_can_atlas_2018: 85/255 (33.33%) · sarcoma_mskcc_2022: 397/2138 (18.57%) |
| MDM2 | 0.28–1.96% | sarc_tcga_pan_can_atlas_2018: 5/255 (1.96%) · sarcoma_mskcc_2022: 6/2138 (0.28%) |
| CDK4 | 0.23–0.39% | sarc_tcga_pan_can_atlas_2018: 1/255 (0.39%) · sarcoma_mskcc_2022: 5/2138 (0.23%) |
| RB1 | 4.63–9.8% | sarc_tcga_pan_can_atlas_2018: 25/255 (9.8%) · sarcoma_mskcc_2022: 99/2138 (4.63%) |
| PDGFRA | 0.39–2.06% | sarc_tcga_pan_can_atlas_2018: 1/255 (0.39%) · sarcoma_mskcc_2022: 44/2138 (2.06%) |
| NTRK1 | 0.47–1.18% | sarc_tcga_pan_can_atlas_2018: 3/255 (1.18%) · sarcoma_mskcc_2022: 10/2138 (0.47%) |
| ALK | 0.7–1.18% | sarc_tcga_pan_can_atlas_2018: 3/255 (1.18%) · sarcoma_mskcc_2022: 15/2138 (0.7%) |
| PDGFRB | 0.8–1.18% | sarc_tcga_pan_can_atlas_2018: 3/255 (1.18%) · sarcoma_mskcc_2022: 17/2138 (0.8%) |
| NF1 | 3.04–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: 65/2138 (3.04%) |
| SS18 | 0.0–0.0% | sarc_tcga_pan_can_atlas_2018: 0/255 (0.0%) · sarcoma_mskcc_2022: not assayed |
| TERT | 0.56–1.57% | sarc_tcga_pan_can_atlas_2018: 4/255 (1.57%) · sarcoma_mskcc_2022: 12/2138 (0.56%) |
| CTAG1B | 0.0–0.0% | sarc_tcga_pan_can_atlas_2018: 0/255 (0.0%) · sarcoma_mskcc_2022: not assayed |
| ATRX | 6.83–14.12% | sarc_tcga_pan_can_atlas_2018: 36/255 (14.12%) · sarcoma_mskcc_2022: 146/2138 (6.83%) |
| SCN2A | 5.1–5.1% | sarc_tcga_pan_can_atlas_2018: 13/255 (5.1%) · sarcoma_mskcc_2022: not assayed |
| FCGBP | 4.31–4.31% | sarc_tcga_pan_can_atlas_2018: 11/255 (4.31%) · sarcoma_mskcc_2022: not assayed |
| SPHKAP | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| PRKDC | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| NAV3 | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| FREM2 | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| DOCK3 | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| CFAP54 | 3.92–3.92% | sarc_tcga_pan_can_atlas_2018: 10/255 (3.92%) · sarcoma_mskcc_2022: not assayed |
| ZAN | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| TRPM6 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| SPTBN4 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| MYO15A | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| MGAM | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| KMT2D | 2.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: 54/2138 (2.53%) |
| FRAS1 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| DOCK2 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| DISP3 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| DCHS2 | 3.53–3.53% | sarc_tcga_pan_can_atlas_2018: 9/255 (3.53%) · sarcoma_mskcc_2022: not assayed |
| WDR87 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| UNC80 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| UNC13C | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| TNRC18 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| TMEM132C | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| SHANK2 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| SCN9A | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| RELN | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| PKHD1 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| PEG3 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| NRXN1 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| MYH7 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| MAP1A | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| LRP1 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| KIAA1549 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| KCNH8 | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| KALRN | 3.14–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: not assayed |
| FAT1 | 1.82–3.14% | sarc_tcga_pan_can_atlas_2018: 8/255 (3.14%) · sarcoma_mskcc_2022: 39/2138 (1.82%) |
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/soft-tissue-sarcoma.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.