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Basal cell carcinoma mutation landscape

How often each gene is altered in basal cell carcinoma, in each sequenced cohort, over the patients on whom it could have been called. Copy number is its own row. Nothing is pooled.

Retrieved 2026-09-18 · Reference cohort: bcc_unige_2016 · JSON: /disease/basal-cell-carcinoma/mutations.json · Back to the briefing

Answer block

In Basal Cell Carcinoma (UNIGE, Nat Genet 2016) (236 sequenced patients, mixed), the most frequently altered of the 48 genes shown are PTCH1 77.97%, TP53 64.83%, TAF1L 58.9%, PCDH15 58.88%, SI 56.07%. Each figure divides by the patients on whom that gene could be called.

48 of 236 patients are hypermutated (more than 920 non-silent mutations, ten times the cohort median of 92); every gene's frequency without them is beside the headline.

Of the briefing's 12 curated targets, 1 are altered in under 2% of this cohort (STK19): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.

1 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%.

Alterationbcc_unige_2016
236 pts · mixed
PTCH1 SNV / small indel77.97%184/236
SMO SNV / small indel27.12%64/236
SUFU SNV / small indel9.32%22/236
GLI1 SNV / small indel11.21%12/107
GLI2 SNV / small indel19.63%21/107
TP53 SNV / small indel64.83%153/236
PTCH2 SNV / small indel14.02%15/107
CDKN2A SNV / small indel5.51%13/236
PDCD1 SNV / small indel3.74%4/107
MYCN SNV / small indel33.47%79/236
PPP6C SNV / small indel16.95%40/236
STK19 SNV / small indel0%
TAF1L SNV / small indel58.9%139/236
ADGRB3 SNV / small indel53.81%127/236
SLIT2 SNV / small indel50.85%120/236
ROS1 SNV / small indel50.42%119/236
GRIN2A SNV / small indel48.31%114/236
PEG3 SNV / small indel44.07%104/236
EPHA3 SNV / small indel41.1%97/236
KDR SNV / small indel40.25%95/236
ERBB4 SNV / small indel39.41%93/236
PREX2 SNV / small indel38.56%91/236
GRM8 SNV / small indel37.71%89/236
EPHA5 SNV / small indel37.71%89/236
ROBO2 SNV / small indel35.59%84/236
EPHA6 SNV / small indel35.59%84/236
DCC SNV / small indel35.17%83/236
NOTCH1 SNV / small indel34.75%82/236
EPHA7 SNV / small indel34.32%81/236
ARID1A SNV / small indel33.47%79/236
LRFN5 SNV / small indel32.63%77/236
TRRAP SNV / small indel30.51%72/236
MYH9 SNV / small indel30.51%72/236
RNF213 SNV / small indel30.08%71/236
NOTCH3 SNV / small indel30.08%71/236
HGF SNV / small indel29.66%70/236
EP400 SNV / small indel29.66%70/236
NOTCH2 SNV / small indel29.24%69/236
TET1 SNV / small indel27.97%66/236
HECW1 SNV / small indel27.97%66/236
SPEN SNV / small indel27.54%65/236
EP300 SNV / small indel27.54%65/236
PTPN14 SNV / small indel26.69%63/236
PCDH15 SNV / small indel58.88%63/107
IGF2R SNV / small indel26.69%63/236
CREBBP SNV / small indel26.69%63/236
SI SNV / small indel56.07%60/107
GRIK2 SNV / small indel25.42%60/236

observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable

Key findings

PTCH1 is mutated in 184 of 236 patients in Basal Cell Carcinoma (UNIGE, Nat Genet 2016).
Numerator: 184 · Denominator: 236 · Frequency: 77.97% · Observed in 1 cohorts · Confidence: low · Source: bcc_unige_2016 · Retrieved: 2026-09-18

TP53 is mutated in 153 of 236 patients in Basal Cell Carcinoma (UNIGE, Nat Genet 2016).
Numerator: 153 · Denominator: 236 · Frequency: 64.83% · Observed in 1 cohorts · Confidence: low · Source: bcc_unige_2016 · Retrieved: 2026-09-18

TAF1L is mutated in 139 of 236 patients in Basal Cell Carcinoma (UNIGE, Nat Genet 2016).
Numerator: 139 · Denominator: 236 · Frequency: 58.9% · Observed in 1 cohorts · Confidence: low · Source: bcc_unige_2016 · Retrieved: 2026-09-18

Gene table — reference cohort

Headline values are from the reference cohort, bcc_unige_2016; 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.

GeneWhy listedLargest alterationAltered / testedFrequencyWithout hypermutatedCohorts observedRange across cohortsRecurrent changes
PTCH1 curated target SNV / small indel 184 / 236 77.97% 76.6% 1 / 1 77.97–77.97% Q576* (n=10), R770* (n=10), P689L (n=5), W1018* (n=5), W236* (n=4)
SMO curated target SNV / small indel 64 / 236 27.12% 27.66% 1 / 1 27.12–27.12% W535L (n=17), L412F (n=9), A459V (n=6), S278I (n=4), S358F (n=3)
SUFU curated target SNV / small indel 22 / 236 9.32% 8.51% 1 / 1 9.32–9.32% R123C (n=5), L98F (n=1), P297S (n=1), G112R (n=1), P281F (n=1)
GLI1 curated target SNV / small indel 12 / 107 11.21% 1.69% 1 / 1 11.21–11.21% L495F (n=1), R100C (n=1), S125F (n=1), Q935* (n=1), S148F (n=1)
GLI2 curated target SNV / small indel 21 / 107 19.63% 15.25% 1 / 1 19.63–19.63% S1120F (n=2), S859F (n=2), P904S (n=1), P712L (n=1), T1499I (n=1)
TP53 curated target SNV / small indel 153 / 236 64.83% 59.04% 1 / 1 64.83–64.83% R213* (n=14), R196* (n=12), Q317* (n=9), R342* (n=9), P177L (n=8)
PTCH2 curated target SNV / small indel 15 / 107 14.02% 3.39% 1 / 1 14.02–14.02% P1166S (n=1), E174* (n=1), Y785H (n=1), P1176S (n=1), F953L (n=1)
CDKN2A curated target SNV / small indel 13 / 236 5.51% 4.26% 1 / 1 5.51–5.51% G6E (n=2), P146S (n=1), G135E (n=1), D108Y (n=1), D74A (n=1)
PDCD1 curated target SNV / small indel 4 / 107 3.74% 0.0% 1 / 1 3.74–3.74% S109I (n=1), R96C (n=1), W32* (n=1), R112K (n=1)
MYCN curated target SNV / small indel 79 / 236 33.47% 31.91% 1 / 1 33.47–33.47% P44L (n=34), P59L (n=17), P44S (n=8), P60S (n=7), P60L (n=6)
PPP6C curated target SNV / small indel 40 / 236 16.95% 15.96% 1 / 1 16.95–16.95% R264C (n=27), P259S (n=4), S270L (n=3), L305F (n=2), D198N (n=1)
STK19 curated target SNV / small indel 0 / 107 0.0% 0.0% 0 / 1 0.0–0.0% none recurrent
TAF1L by frequency SNV / small indel 139 / 236 58.9% 54.26% 1 / 1 58.9–58.9% R254* (n=11), R793W (n=6), R1205Q (n=5), S926F (n=5), R845Q (n=4)
ADGRB3 by frequency SNV / small indel 127 / 236 53.81% 45.74% 1 / 1 53.81–53.81% G972E (n=15), E659K (n=8), R1418Q (n=6), M1361I (n=6), G494E (n=4)
SLIT2 by frequency SNV / small indel 120 / 236 50.85% 45.74% 1 / 1 50.85–50.85% S373F (n=7), G715E (n=4), R828Q (n=3), R1216C (n=3), G1201S (n=3)
ROS1 by frequency SNV / small indel 119 / 236 50.42% 44.15% 1 / 1 50.42–50.42% P1120L (n=3), G705E (n=3), R2126W (n=3), Q237* (n=3), P105L (n=3)
GRIN2A by frequency SNV / small indel 114 / 236 48.31% 42.02% 1 / 1 48.31–48.31% E962K (n=8), G1322E (n=5), M653I (n=4), E806K (n=4), S616F (n=3)
PEG3 by frequency SNV / small indel 104 / 236 44.07% 38.83% 1 / 1 44.07–44.07% E747K (n=7), E1352K (n=5), S773L (n=4), E628K (n=4), R50W (n=4)
EPHA3 by frequency SNV / small indel 97 / 236 41.1% 35.11% 1 / 1 41.1–41.1% R136* (n=8), E615K (n=7), E930K (n=4), G783R (n=4), R324Q (n=3)
KDR by frequency SNV / small indel 95 / 236 40.25% 38.3% 1 / 1 40.25–40.25% R1032Q (n=6), S1100F (n=4), S178F (n=4), G509E (n=4), R944Q (n=3)
ERBB4 by frequency SNV / small indel 93 / 236 39.41% 32.45% 1 / 1 39.41–39.41% R711C (n=9), R544W (n=6), R114Q (n=4), D843N (n=4), R992C (n=3)
PREX2 by frequency SNV / small indel 91 / 236 38.56% 36.17% 1 / 1 38.56–38.56% R297C (n=4), P776S (n=2), R117C (n=2), G1417E (n=2), P1058S (n=2)
GRM8 by frequency SNV / small indel 89 / 236 37.71% 31.91% 1 / 1 37.71–37.71% G873E (n=12), W215* (n=5), G726E (n=3), G340E (n=3), G628E (n=3)
EPHA5 by frequency SNV / small indel 89 / 236 37.71% 35.11% 1 / 1 37.71–37.71% E149K (n=6), P841S (n=6), G287E (n=4), P141S (n=3), R553Q (n=3)
ROBO2 by frequency SNV / small indel 84 / 236 35.59% 32.45% 1 / 1 35.59–35.59% R261C (n=6), P46S (n=4), I614T (n=4), R335W (n=3), G202R (n=3)
EPHA6 by frequency SNV / small indel 84 / 236 35.59% 32.98% 1 / 1 35.59–35.59% G453E (n=3), G231R (n=3), R268C (n=3), R182C (n=3), G629E (n=2)
DCC by frequency SNV / small indel 83 / 236 35.17% 27.66% 1 / 1 35.17–35.17% G407E (n=4), E403K (n=3), G84E (n=2), R1337* (n=2), G54E (n=2)
NOTCH1 by frequency SNV / small indel 82 / 236 34.75% 31.38% 1 / 1 34.75–34.75% S137L (n=4), P1275S (n=4), P1770S (n=3), E455K (n=3), P460S (n=2)
EPHA7 by frequency SNV / small indel 81 / 236 34.32% 30.85% 1 / 1 34.32–34.32% S49F (n=4), E715K (n=3), S225F (n=3), G565R (n=2), P443S (n=2)
ARID1A by frequency SNV / small indel 79 / 236 33.47% 29.26% 1 / 1 33.47–33.47% S2113F (n=3), Q1458* (n=3), Q1473* (n=2), E2224* (n=2), Q546* (n=2)
LRFN5 by frequency SNV / small indel 77 / 236 32.63% 29.79% 1 / 1 32.63–32.63% R99Q (n=11), S139F (n=5), S400F (n=3), R645K (n=3), E597K (n=2)
TRRAP by frequency SNV / small indel 72 / 236 30.51% 25.53% 1 / 1 30.51–30.51% S2051F (n=2), E1248K (n=2), R1447C (n=2), P498S (n=2), P2815S (n=2)
MYH9 by frequency SNV / small indel 72 / 236 30.51% 27.13% 1 / 1 30.51–30.51% P591L (n=7), P392S (n=7), R263C (n=5), A416V (n=4), P535S (n=4)
RNF213 by frequency SNV / small indel 71 / 236 30.08% 26.6% 1 / 1 30.08–30.08% S739F (n=3), P111S (n=2), A1844T (n=2), P948L (n=2), A4530V (n=2)
NOTCH3 by frequency SNV / small indel 71 / 236 30.08% 27.66% 1 / 1 30.08–30.08% P1424L (n=3), P1026S (n=2), P2261L (n=2), S2203F (n=2), A1852T (n=2)
HGF by frequency SNV / small indel 70 / 236 29.66% 26.06% 1 / 1 29.66–29.66% E174K (n=5), R393C (n=4), E183K (n=4), R178Q (n=3), S45L (n=3)
EP400 by frequency SNV / small indel 70 / 236 29.66% 25.53% 1 / 1 29.66–29.66% R2408C (n=7), S2884F (n=3), P1455L (n=2), P602L (n=2), P126L (n=2)
NOTCH2 by frequency SNV / small indel 69 / 236 29.24% 22.87% 1 / 1 29.24–29.24% P394L (n=3), R1838* (n=2), S204F (n=2), P2371S (n=2), R1786* (n=2)
TET1 by frequency SNV / small indel 66 / 236 27.97% 22.87% 1 / 1 27.97–27.97% P1207S (n=4), P859S (n=3), P1008L (n=2), P253S (n=2), P749S (n=2)
HECW1 by frequency SNV / small indel 66 / 236 27.97% 23.94% 1 / 1 27.97–27.97% S721F (n=3), R40* (n=2), V305I (n=2), E586K (n=2), S66F (n=2)
SPEN by frequency SNV / small indel 65 / 236 27.54% 22.87% 1 / 1 27.54–27.54% P3249L (n=3), P1738S (n=2), P1858S (n=2), A2251T (n=2), E2012* (n=2)
EP300 by frequency SNV / small indel 65 / 236 27.54% 26.06% 1 / 1 27.54–27.54% P846L (n=2), L242F (n=2), P500S (n=2), P593S (n=2), R1137Q (n=1)
PTPN14 by frequency SNV / small indel 63 / 236 26.69% 24.47% 1 / 1 26.69–26.69% R1045* (n=6), Q610* (n=3), P745S (n=2), X330_splice (n=2), Q343* (n=2)
PCDH15 by frequency SNV / small indel 63 / 107 58.88% 35.59% 1 / 1 58.88–58.88% E1570K (n=3), R764C (n=3), E1533K (n=3), E1467K (n=2), R336Q (n=2)
IGF2R by frequency SNV / small indel 63 / 236 26.69% 22.87% 1 / 1 26.69–26.69% P1716S (n=4), D441N (n=2), P298L (n=2), S553F (n=2), T1073I (n=2)
CREBBP by frequency SNV / small indel 63 / 236 26.69% 25.53% 1 / 1 26.69–26.69% P225R (n=3), R1392* (n=2), Q733* (n=2), S1680del (n=2), S2338F (n=2)
SI by frequency SNV / small indel 60 / 107 56.07% 40.68% 1 / 1 56.07–56.07% P579S (n=4), M1464I (n=3), M392I (n=2), G603R (n=2), D1380N (n=2)
GRIK2 by frequency SNV / small indel 60 / 236 25.42% 22.34% 1 / 1 25.42–25.42% E479K (n=4), R458* (n=3), R431C (n=3), G382S (n=2), R468K (n=2)

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.

CohortAccessionPatientsSamples sequenced / in studyAssayPanels (samples)BuildProfiles readHypermutated patientsMedian mutations / sample
Basal Cell Carcinoma (UNIGE, Nat Genet 2016) reference
Basal Cell Carcinoma (UNIGE, Nat Genet 2016)
bcc_unige_2016236 observed293 / 293mixedbcc_unige_2016_cancer_panel (167), WES (126)hg19SNV, small indel4892

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.

GeneEventObserved patientsTested patientsFrequencyCohortProfile
No copy-number profile reached 2% for any listed gene, or no cohort carries one.

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.

GeneRangePer cohort (altered / tested)
PTCH177.97–77.97%bcc_unige_2016: 184/236 (77.97%)
SMO27.12–27.12%bcc_unige_2016: 64/236 (27.12%)
SUFU9.32–9.32%bcc_unige_2016: 22/236 (9.32%)
GLI111.21–11.21%bcc_unige_2016: 12/107 (11.21%)
GLI219.63–19.63%bcc_unige_2016: 21/107 (19.63%)
TP5364.83–64.83%bcc_unige_2016: 153/236 (64.83%)
PTCH214.02–14.02%bcc_unige_2016: 15/107 (14.02%)
CDKN2A5.51–5.51%bcc_unige_2016: 13/236 (5.51%)
PDCD13.74–3.74%bcc_unige_2016: 4/107 (3.74%)
MYCN33.47–33.47%bcc_unige_2016: 79/236 (33.47%)
PPP6C16.95–16.95%bcc_unige_2016: 40/236 (16.95%)
STK190.0–0.0%bcc_unige_2016: 0/107 (0.0%)
TAF1L58.9–58.9%bcc_unige_2016: 139/236 (58.9%)
ADGRB353.81–53.81%bcc_unige_2016: 127/236 (53.81%)
SLIT250.85–50.85%bcc_unige_2016: 120/236 (50.85%)
ROS150.42–50.42%bcc_unige_2016: 119/236 (50.42%)
GRIN2A48.31–48.31%bcc_unige_2016: 114/236 (48.31%)
PEG344.07–44.07%bcc_unige_2016: 104/236 (44.07%)
EPHA341.1–41.1%bcc_unige_2016: 97/236 (41.1%)
KDR40.25–40.25%bcc_unige_2016: 95/236 (40.25%)
ERBB439.41–39.41%bcc_unige_2016: 93/236 (39.41%)
PREX238.56–38.56%bcc_unige_2016: 91/236 (38.56%)
GRM837.71–37.71%bcc_unige_2016: 89/236 (37.71%)
EPHA537.71–37.71%bcc_unige_2016: 89/236 (37.71%)
ROBO235.59–35.59%bcc_unige_2016: 84/236 (35.59%)
EPHA635.59–35.59%bcc_unige_2016: 84/236 (35.59%)
DCC35.17–35.17%bcc_unige_2016: 83/236 (35.17%)
NOTCH134.75–34.75%bcc_unige_2016: 82/236 (34.75%)
EPHA734.32–34.32%bcc_unige_2016: 81/236 (34.32%)
ARID1A33.47–33.47%bcc_unige_2016: 79/236 (33.47%)
LRFN532.63–32.63%bcc_unige_2016: 77/236 (32.63%)
TRRAP30.51–30.51%bcc_unige_2016: 72/236 (30.51%)
MYH930.51–30.51%bcc_unige_2016: 72/236 (30.51%)
RNF21330.08–30.08%bcc_unige_2016: 71/236 (30.08%)
NOTCH330.08–30.08%bcc_unige_2016: 71/236 (30.08%)
HGF29.66–29.66%bcc_unige_2016: 70/236 (29.66%)
EP40029.66–29.66%bcc_unige_2016: 70/236 (29.66%)
NOTCH229.24–29.24%bcc_unige_2016: 69/236 (29.24%)
TET127.97–27.97%bcc_unige_2016: 66/236 (27.97%)
HECW127.97–27.97%bcc_unige_2016: 66/236 (27.97%)
SPEN27.54–27.54%bcc_unige_2016: 65/236 (27.54%)
EP30027.54–27.54%bcc_unige_2016: 65/236 (27.54%)
PTPN1426.69–26.69%bcc_unige_2016: 63/236 (26.69%)
PCDH1558.88–58.88%bcc_unige_2016: 63/107 (58.88%)
IGF2R26.69–26.69%bcc_unige_2016: 63/236 (26.69%)
CREBBP26.69–26.69%bcc_unige_2016: 63/236 (26.69%)
SI56.07–56.07%bcc_unige_2016: 60/107 (56.07%)
GRIK225.42–25.42%bcc_unige_2016: 60/236 (25.42%)

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

How a machine should read this page

  1. Denominators: every frequency divides by the patients in one named cohort on whom the gene could be called; there is no disease-wide figure.
  2. Missing values: not_assayed (the panel did not carry the gene), not_observed (assayed, none found) and not_evaluable (the cohort could not be read) are three different facts and are never converted to zero.
  3. Counting: patients, not samples; several samples from one patient count once. Non-silent calls only.
  4. Copy number: a separate assay with a separate roster; discrete calls at ±2 only.
  5. Hypermutation: flagged per cohort; the headline keeps all patients and the frequency without them is reported beside it.
  6. 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/basal-cell-carcinoma.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.