Disease intelligence · mutation landscape
Thyroid cancer mutation landscape
How often each gene is altered in thyroid 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 Thyroid Carcinoma (TCGA, PanCancer Atlas) (489 sequenced patients, exome or genome), the most frequently altered of the 49 genes shown are BRAF 58.49%, NRAS 7.98%, TG 3.89%, HRAS 3.27%, ZFHX3 1.84%. Each figure divides by the patients on whom that gene could be called.
6 of 489 patients are hypermutated (more than 100 non-silent mutations, ten times the cohort median of 10); every gene's frequency without them is beside the headline.
Of the briefing's 12 curated targets, 9 are altered in under 2% of this cohort (RET, TERT, TP53, NTRK1, ALK, PIK3CA, TSHR, SLC5A5, PAX8): 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 | thca_tcga_pan_can_atlas_2018 489 pts · exome or genome | thyroid_mskcc_2016 117 pts · mixed |
|---|---|---|
| BRAF SNV / small indel | 58.49%286/489 | 36.75%43/117 |
| RET SNV / small indel | 0.2%1/489 | 0% |
| NRAS SNV / small indel | 7.98%39/489 | 21.37%25/117 |
| HRAS SNV / small indel | 3.27%16/489 | 5.13%6/117 |
| TERT SNV / small indel | 0.61%3/489 | 0.85%1/117 |
| TP53 SNV / small indel | 0.41%2/489 | 25.64%30/117 |
| TP53 deep deletion | 0.4%2/497 | 3.42%4/117 |
| NTRK1 SNV / small indel | 0% | 0.85%1/117 |
| ALK SNV / small indel | 0.2%1/489 | 0.85%1/117 |
| PIK3CA SNV / small indel | 0.82%4/489 | 6.84%8/117 |
| TSHR SNV / small indel | 0.2%1/489 | 4.27%5/117 |
| SLC5A5 SNV / small indel | 0.2%1/489 | 0% |
| PAX8 SNV / small indel | 0.2%1/489 | 0% |
| TG SNV / small indel | 3.89%19/489 | 0% |
| ZFHX3 SNV / small indel | 1.84%9/489 | 0% |
| KMT2A SNV / small indel | 1.43%7/489 | 5.13%6/117 |
| EIF1AX SNV / small indel | 1.43%7/489 | 10.26%12/117 |
| COL5A3 SNV / small indel | 1.43%7/489 | 0% |
| PIK3R5 SNV / small indel | 1.23%6/489 | 0% |
| KMT2C SNV / small indel | 1.23%6/489 | 2.56%3/117 |
| ITPR2 SNV / small indel | 1.23%6/489 | 0% |
| ATM SNV / small indel | 1.23%6/489 | 8.55%10/117 |
| USP9X SNV / small indel | 1.02%5/489 | 0% |
| TENM2 SNV / small indel | 1.02%5/489 | 0% |
| TACC2 SNV / small indel | 1.02%5/489 | 0% |
| SHROOM2 SNV / small indel | 1.02%5/489 | 0% |
| PTPRZ1 SNV / small indel | 1.02%5/489 | 0% |
| PKHD1 SNV / small indel | 1.02%5/489 | 0% |
| PDZD2 SNV / small indel | 1.02%5/489 | 0% |
| NAV3 SNV / small indel | 1.02%5/489 | 0% |
| LTBP2 SNV / small indel | 1.02%5/489 | 0% |
| LAMA4 SNV / small indel | 1.02%5/489 | 0% |
| HSPG2 SNV / small indel | 1.02%5/489 | 0% |
| GBF1 SNV / small indel | 1.02%5/489 | 0% |
| FBN1 SNV / small indel | 1.02%5/489 | 0% |
| DNMT3A SNV / small indel | 1.02%5/489 | 1.71%2/117 |
| COL7A1 SNV / small indel | 1.02%5/489 | 0% |
| BPTF SNV / small indel | 1.02%5/489 | 0% |
| BDP1 SNV / small indel | 1.02%5/489 | 0% |
| ALPK3 SNV / small indel | 1.02%5/489 | 0% |
| AKT1 SNV / small indel | 1.02%5/489 | 0% |
| ZC3H13 SNV / small indel | 0.82%4/489 | 0% |
| WNK2 SNV / small indel | 0.82%4/489 | 0% |
| WDR33 SNV / small indel | 0.82%4/489 | 0% |
| VPS13D SNV / small indel | 0.82%4/489 | 0% |
| UGGT2 SNV / small indel | 0.82%4/489 | 0% |
| UBQLN2 SNV / small indel | 0.82%4/489 | 0% |
| THBS2 SNV / small indel | 0.82%4/489 | 0% |
| TENM4 SNV / small indel | 0.82%4/489 | 0% |
| STOX2 SNV / small indel | 0.82%4/489 | 0% |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
BRAF is mutated in 286 of 489 patients in Thyroid Carcinoma (TCGA, PanCancer Atlas).
NRAS is mutated in 39 of 489 patients in Thyroid Carcinoma (TCGA, PanCancer Atlas).
TG is mutated in 19 of 489 patients in Thyroid Carcinoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
Headline values are from the reference cohort, thca_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 |
|---|---|---|---|---|---|---|---|---|
| BRAF | curated target | SNV / small indel | 286 / 489 | 58.49% | 58.8% | 2 / 2 | 36.75–58.49% | V600E (n=284), K601E (n=2), P490_Q494del (n=1) |
| RET | curated target | deep deletion | 2 / 497 | 0.4% mutation 0.2% | 0.21% | 1 / 2 | 0.0–0.2% | V945M (n=1) |
| NRAS | curated target | SNV / small indel | 39 / 489 | 7.98% | 7.66% | 2 / 2 | 7.98–21.37% | Q61R (n=31), Q61K (n=8) |
| HRAS | curated target | SNV / small indel | 16 / 489 | 3.27% | 3.11% | 2 / 2 | 3.27–5.13% | Q61R (n=13), Q61K (n=3) |
| TERT | curated target | SNV / small indel | 3 / 489 | 0.61% | 0.62% | 2 / 2 | 0.61–0.85% | R470H (n=1), T1113Lfs*62 (n=1), S602L (n=1) |
| TP53 | curated target | SNV / small indel | 2 / 489 | 0.41% | 0.41% | 2 / 2 | 0.41–25.64% | Q375* (n=1), Q192* (n=1) |
| NTRK1 | curated target | deep deletion | 1 / 497 | 0.2% mutation 0.0% | 0.0% | 1 / 2 | 0.0–0.85% | none recurrent |
| ALK | curated target | SNV / small indel | 1 / 489 | 0.2% | 0.21% | 2 / 2 | 0.2–0.85% | P693S (n=1) |
| PIK3CA | curated target | SNV / small indel | 4 / 489 | 0.82% | 0.83% | 2 / 2 | 0.82–6.84% | M1043I (n=1), E110del (n=1), E674* (n=1), G118D (n=1) |
| TSHR | curated target | SNV / small indel | 1 / 489 | 0.2% | 0.21% | 2 / 2 | 0.2–4.27% | M453T (n=1) |
| SLC5A5 | curated target | SNV / small indel | 1 / 489 | 0.2% | 0.21% | 1 / 2 | 0.0–0.2% | A581G (n=1) |
| PAX8 | curated target | SNV / small indel | 1 / 489 | 0.2% | 0.21% | 1 / 2 | 0.0–0.2% | P235Q (n=1) |
| TG | by frequency | SNV / small indel | 19 / 489 | 3.89% | 3.93% | 1 / 2 | 0.0–3.89% | S1619Hfs*12 (n=1), L2282Ifs*61 (n=1), Q1246P (n=1), C1306S (n=1), Q1515del (n=1) |
| ZFHX3 | by frequency | SNV / small indel | 9 / 489 | 1.84% | 1.86% | 1 / 2 | 0.0–1.84% | K1572Rfs*19 (n=2), G1022D (n=1), H1571R (n=1), R2161W (n=1), R2988Efs*33 (n=1) |
| KMT2A | by frequency | SNV / small indel | 7 / 489 | 1.43% | 1.24% | 2 / 2 | 1.43–5.13% | D2721V (n=1), S3518F (n=1), S3518A (n=1), Q3624H (n=1), N1656T (n=1) |
| EIF1AX | by frequency | SNV / small indel | 7 / 489 | 1.43% | 1.45% | 2 / 2 | 1.43–10.26% | G9D (n=2), X113_splice (n=2), A113V (n=1), G9R (n=1), G8R (n=1) |
| COL5A3 | by frequency | SNV / small indel | 7 / 489 | 1.43% | 1.04% | 1 / 2 | 0.0–1.43% | R219W (n=1), P606H (n=1), Q236E (n=1), G1388C (n=1), R1644H (n=1) |
| PIK3R5 | by frequency | SNV / small indel | 6 / 489 | 1.23% | 1.04% | 1 / 2 | 0.0–1.23% | K104E (n=1), Q555H (n=1), A666V (n=1), D76N (n=1), Y291* (n=1) |
| KMT2C | by frequency | SNV / small indel | 6 / 489 | 1.23% | 1.24% | 2 / 2 | 1.23–2.56% | Q3591* (n=1), S3213L (n=1), S888F (n=1), C394S (n=1), K3847N (n=1) |
| ITPR2 | by frequency | SNV / small indel | 6 / 489 | 1.23% | 1.24% | 1 / 2 | 0.0–1.23% | E975V (n=1), M1576I (n=1), V483I (n=1), R780H (n=1), A2351V (n=1) |
| ATM | by frequency | SNV / small indel | 6 / 489 | 1.23% | 1.24% | 2 / 2 | 1.23–8.55% | D2997G (n=1), E16Nfs*18 (n=1), T1908Kfs*9 (n=1), W2845C (n=1), L2132V (n=1) |
| USP9X | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | K1798T (n=1), P1105Tfs*4 (n=1), X1535_splice (n=1), E61* (n=1), P1083A (n=1) |
| TENM2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.62% | 1 / 2 | 0.0–1.02% | P997Q (n=1), D904Y (n=1), P1801H (n=1), I1803T (n=1), A1538V (n=1) |
| TACC2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 1 / 2 | 0.0–1.02% | G438_S439dup (n=1), A1255S (n=1), M200V (n=1), R606H (n=1), R2728S (n=1) |
| SHROOM2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 1 / 2 | 0.0–1.02% | R1452L (n=1), P822Q (n=1), L1585P (n=1), N297S (n=1), P1352T (n=1) |
| PTPRZ1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | T846I (n=1), L1673V (n=1), P818H (n=1), F363V (n=1), E2210Q (n=1) |
| PKHD1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | T2850K (n=1), R2891C (n=1), W664L (n=1), L1190F (n=1), S1066L (n=1) |
| PDZD2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | A1296E (n=1), P680R (n=1), G269S (n=1), T1142* (n=1), G313C (n=1) |
| NAV3 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 1 / 2 | 0.0–1.02% | Q563P (n=1), T1340I (n=1), P2035S (n=1), P208H (n=1), S791Y (n=1) |
| LTBP2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.62% | 1 / 2 | 0.0–1.02% | L1202P (n=1), P843T (n=1), P1471H (n=1), P537T (n=1), A1407V (n=1) |
| LAMA4 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 1 / 2 | 0.0–1.02% | P1785H (n=1), A594E (n=1), N810K (n=1), R392M (n=1), D783V (n=1) |
| HSPG2 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.62% | 1 / 2 | 0.0–1.02% | E4141* (n=1), I1056T (n=1), R1523S (n=1), G4345W (n=1), S4171Y (n=1) |
| GBF1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | N1308I (n=1), C360Y (n=1), X1626_splice (n=1), D762* (n=1), X1548_splice (n=1) |
| FBN1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 1 / 2 | 0.0–1.02% | E571K (n=1), G486V (n=1), G276E (n=1), E806K (n=1), G90W (n=1) |
| DNMT3A | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.83% | 2 / 2 | 1.02–1.71% | W313* (n=1), K589N (n=1), P195L (n=1), K766Efs*15 (n=1), E240Sfs*8 (n=1) |
| COL7A1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.62% | 1 / 2 | 0.0–1.02% | A2830T (n=1), G316W (n=1), R1724S (n=1), X2180_splice (n=1), Q1924H (n=1) |
| BPTF | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | M1399V (n=1), D586H (n=1), P1476S (n=1), E2424* (n=1), T778N (n=1) |
| BDP1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | M905T (n=1), P1932A (n=1), P2231S (n=1), Q779* (n=1), Q2571* (n=1) |
| ALPK3 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 0.62% | 1 / 2 | 0.0–1.02% | Q1904K (n=1), Q424* (n=1), A1252T (n=1), H748N (n=1), G1094W (n=1) |
| AKT1 | by frequency | SNV / small indel | 5 / 489 | 1.02% | 1.04% | 1 / 2 | 0.0–1.02% | E17K (n=3), E133D (n=1), L52R (n=1) |
| ZC3H13 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.62% | 1 / 2 | 0.0–0.82% | R384G (n=1), P1035H (n=1), E28V (n=1), R646* (n=1) |
| WNK2 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.83% | 1 / 2 | 0.0–0.82% | S2123N (n=1), P1555A (n=1), H422Y (n=1), P793L (n=1) |
| WDR33 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.62% | 1 / 2 | 0.0–0.82% | P587R (n=1), S1210C (n=1), D1137N (n=1), G980W (n=1) |
| VPS13D | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.83% | 1 / 2 | 0.0–0.82% | L1671V (n=1), N3247K (n=1), A2597G (n=1), X2733_splice (n=1) |
| UGGT2 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.62% | 1 / 2 | 0.0–0.82% | L14Q (n=1), N787T (n=1), W1488C (n=1), E786D (n=1) |
| UBQLN2 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.41% | 1 / 2 | 0.0–0.82% | R309S (n=2), P573S (n=1), P414Q (n=1) |
| THBS2 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.41% | 1 / 2 | 0.0–0.82% | R460C (n=1), G94C (n=1), G773V (n=1), G247S (n=1) |
| TENM4 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.62% | 1 / 2 | 0.0–0.82% | E1004* (n=1), E1162K (n=1), P1510H (n=1), A2587S (n=1) |
| STOX2 | by frequency | SNV / small indel | 4 / 489 | 0.82% | 0.62% | 1 / 2 | 0.0–0.82% | Q70* (n=1), G267W (n=1), S240R (n=1), P638T (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 |
|---|---|---|---|---|---|---|---|---|---|
| Thyroid Carcinoma (TCGA, PanCancer Atlas) reference | thca_tcga_pan_can_atlas_2018 | 489 observed | 490 / 500 | exome or genome | WES (490) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 6 | 10.0 |
| Poorly-Differentiated and Anaplastic Thyroid Cancers (MSK, JCI 2016) | thyroid_mskcc_2016 | 117 observed | 117 / 117 | mixed | WES (82), IMPACT341 (35) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 2 |
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 |
|---|---|---|---|---|---|---|
| TP53 | deep deletion | 4 | 117 | 3.42% | thyroid_mskcc_2016 | thyroid_mskcc_2016_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) |
|---|---|---|
| BRAF | 36.75–58.49% | thca_tcga_pan_can_atlas_2018: 286/489 (58.49%) · thyroid_mskcc_2016: 43/117 (36.75%) |
| RET | 0.0–0.2% | thca_tcga_pan_can_atlas_2018: 1/489 (0.2%) · thyroid_mskcc_2016: 0/117 (0.0%) |
| NRAS | 7.98–21.37% | thca_tcga_pan_can_atlas_2018: 39/489 (7.98%) · thyroid_mskcc_2016: 25/117 (21.37%) |
| HRAS | 3.27–5.13% | thca_tcga_pan_can_atlas_2018: 16/489 (3.27%) · thyroid_mskcc_2016: 6/117 (5.13%) |
| TERT | 0.61–0.85% | thca_tcga_pan_can_atlas_2018: 3/489 (0.61%) · thyroid_mskcc_2016: 1/117 (0.85%) |
| TP53 | 0.41–25.64% | thca_tcga_pan_can_atlas_2018: 2/489 (0.41%) · thyroid_mskcc_2016: 30/117 (25.64%) |
| NTRK1 | 0.0–0.85% | thca_tcga_pan_can_atlas_2018: 0/489 (0.0%) · thyroid_mskcc_2016: 1/117 (0.85%) |
| ALK | 0.2–0.85% | thca_tcga_pan_can_atlas_2018: 1/489 (0.2%) · thyroid_mskcc_2016: 1/117 (0.85%) |
| PIK3CA | 0.82–6.84% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 8/117 (6.84%) |
| TSHR | 0.2–4.27% | thca_tcga_pan_can_atlas_2018: 1/489 (0.2%) · thyroid_mskcc_2016: 5/117 (4.27%) |
| SLC5A5 | 0.0–0.2% | thca_tcga_pan_can_atlas_2018: 1/489 (0.2%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| PAX8 | 0.0–0.2% | thca_tcga_pan_can_atlas_2018: 1/489 (0.2%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| TG | 0.0–3.89% | thca_tcga_pan_can_atlas_2018: 19/489 (3.89%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| ZFHX3 | 0.0–1.84% | thca_tcga_pan_can_atlas_2018: 9/489 (1.84%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| KMT2A | 1.43–5.13% | thca_tcga_pan_can_atlas_2018: 7/489 (1.43%) · thyroid_mskcc_2016: 6/117 (5.13%) |
| EIF1AX | 1.43–10.26% | thca_tcga_pan_can_atlas_2018: 7/489 (1.43%) · thyroid_mskcc_2016: 12/117 (10.26%) |
| COL5A3 | 0.0–1.43% | thca_tcga_pan_can_atlas_2018: 7/489 (1.43%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| PIK3R5 | 0.0–1.23% | thca_tcga_pan_can_atlas_2018: 6/489 (1.23%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| KMT2C | 1.23–2.56% | thca_tcga_pan_can_atlas_2018: 6/489 (1.23%) · thyroid_mskcc_2016: 3/117 (2.56%) |
| ITPR2 | 0.0–1.23% | thca_tcga_pan_can_atlas_2018: 6/489 (1.23%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| ATM | 1.23–8.55% | thca_tcga_pan_can_atlas_2018: 6/489 (1.23%) · thyroid_mskcc_2016: 10/117 (8.55%) |
| USP9X | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| TENM2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| TACC2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| SHROOM2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| PTPRZ1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| PKHD1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| PDZD2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| NAV3 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| LTBP2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| LAMA4 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| HSPG2 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| GBF1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| FBN1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| DNMT3A | 1.02–1.71% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 2/117 (1.71%) |
| COL7A1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| BPTF | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| BDP1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| ALPK3 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| AKT1 | 0.0–1.02% | thca_tcga_pan_can_atlas_2018: 5/489 (1.02%) · thyroid_mskcc_2016: 0/117 (0.0%) |
| ZC3H13 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| WNK2 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| WDR33 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| VPS13D | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| UGGT2 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| UBQLN2 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| THBS2 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| TENM4 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
| STOX2 | 0.0–0.82% | thca_tcga_pan_can_atlas_2018: 4/489 (0.82%) · thyroid_mskcc_2016: 0/82 (0.0%) |
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/thyroid-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.