Q (sonnet): I receive a report with the PIK3CA p.*1069Wext*3 mutation. Can you provide details of it

▶ list_guides
{}

◀ result
{"result":[{"uri":"cbioportal://mutation-frequency-guide","description":"Comprehensive guide for calculating gene mutation frequencies with gene-specific profiling denominators"},{"uri":"cbioportal://clinical-data-guide","description":"Guide for querying clinical data including patient vs sample level considerations"},{"uri":"cbioportal://sample-filtering-guide","description":"Guide for filtering samples and studies in cBioPortal queries"},{"uri":"cbioportal://common-pitfalls","description":"Guide to avoid common mistakes when querying cBioPortal data. If you already know which numbered pitfall applies, fetch just that section via read_guide(\"cbioportal://common-pitfalls#<number>\") (e.g. #16) instead of the full guide"},{"uri":"cbioportal://treatment-guide","description":"Guide for querying treatment/clinical event data including drug agents, timelines, and linking to genomic data"},{"uri":"cbioportal://faq-guide","description":"General cBioPortal FAQ: history, how to cite, data types, reference genome, abbreviations, GISTIC thresholds, API access"},{"uri":"cbioportal://statistical-tests-guide","description":"Statistical test selection guide — decision matrix for choosing Fisher's exact, Wilcoxon, chi-squared, t-test, ANOVA, etc. based on data type and group count"},{"uri":"cbioportal://gene-expression-guide","description":"Gene expression / copy-number / methylation analysis. Covers genetic_alteration_derived, profile_type discovery, and the gene_pair_coexpression view for Spearman correlation between two genes"},{"uri":"cbioportal://external-resources-guide","description":"Guide for finding external linked resources such as imaging, pathology, Minerva, HTAN, or other resource_* table links before declaring data unavailable"},{"uri":"cbioportal://gene-resolution-guide","description":"Guide for resolving ambiguous gene symbols, aliases, gene families, and shorthand such as CD3 before querying expression or alteration data"},{"uri":"cbioportal://study-resolution-guide","description":"Guide for resolving requested studies, avoiding silent substitute cohorts, and redirecting to known external cBioPortal instances when data is not in this deployment"},{"uri":"cbioportal://germline-guide","description":"Guide for querying germline variant data — storage columns, study discovery, query patterns, and somatic vs germline considerations"},{"uri":"cbioportal://study-guide/{study_id}","description":"Dynamic study-specific guide - use get_study_guide(study_id) tool to generate"}]}

▶ read_guide
{
 "uri": "cbioportal://common-pitfalls#16"
}

▶ read_guide
{
 "uri": "cbioportal://mutation-frequency-guide"
}

◀ result
### 16. 🚨 SILENT QUERY SUBSTITUTION ("did you mean...")

When the user's wording differs from canonical terminology (e.g. "V600V" looks like "V600E" with a typo, or "point mutation" sounds like "missense"), it is forbidden to silently rewrite the question and answer the rewritten version. Doing so produces an answer that looks confident but is for a different question — the user cannot tell what was changed.

#### ❌ Wrong: silently substitute

> User: *"Find patients in colorectal cancer with the V600V alteration in BRAF"*
> Agent: *(internally treats this as V600E)* "I found 412 samples with BRAF V600E in colorectal studies..."

> User: *"What is the most prevalent TP53 mutation in uterine cancer that is not a point mutation?"*
> Agent: *(internally treats "point mutation" = "missense", silently excludes only missense)* "The most prevalent non-missense TP53 mutation is..."

#### ✅ Correct: answer the literal question, flag any normalization

For an unusual-looking variant the user may have typed deliberately:
- Query for what was asked, literally.
- If 0 rows come back, **explain *why* zero is the expected answer** before suggesting a likely-intended alternative. For synonymous variants (e.g. BRAF V600V, TP53 R175R), the explanation is: *cBioPortal's mutation tables filter out synonymous (silent) variants in most studies, so 0 hits means "filtered upstream", not "no such variant exists in any patient"*. Then ask: *"Did you mean V600E (the canonical activating variant)? Or would you like me to look for V600V in the studies that do retain synonymous calls?"*
- If the wording is ambiguous (e.g. "point mutation"), ask the user which definition they meant before querying — do not pick one silently.

#### Mutation-type terminology mapping (use this to disambiguate)

| User says | Canonical definition | `mutation_type` filter |
|---|---|---|
| "point mutation" | Any SNV (single-nucleotide variant) — includes missense, nonsense, synonymous, splice-site SNVs | `mutation_type IN ('Missense_Mutation','Nonsense_Mutation','Silent','Splice_Site')` — **but ask the user to confirm scope first** |
| "missense" | Single amino-acid substitution that changes the protein | `mutation_type = 'Missense_Mutation'` |
| "nonsense" / "stop-gain" | Premature stop codon | `mutation_type = 'Nonsense_Mutation'` |
| "synonymous" / "silent" | Nucleotide change with no amino-acid change | `mutation_type = 'Silent'` (**often filtered out of public datasets** — see below) |
| "splice site" | Mutation in canonical splice acceptor/donor | `mutation_type = 'Splice_Site'` |
| "frameshift" | Indel changing reading frame | `mutation_type IN ('Frame_Shift_Ins','Frame_Shift_Del')` |
| "indel" / "in-frame" | In-frame insertion or deletion | `mutation_type IN ('In_Frame_Ins','In_Frame_Del')` |
| "truncating" | Anything that disrupts the protein early | `mutation_type IN ('Nonsense_Mutation','Frame_Shift_Ins','Frame_Shift_Del','Splice_Site','Nonstop_Mutation')` |

**Synonymous-variant filter. … (785 more chars)

◀ result
# Mutation Frequency Analysis Guide

## IMPORTANT: Reporting Mutation Frequencies
- **ALWAYS report frequencies as percentages**, not raw counts: `frequency = (altered_samples / total_profiled_samples) × 100`
- For quick frequency lookups, **prefer the TCGA Pan-Cancer Atlas study first**, then offer to expand to other studies
- When reporting across multiple studies, show **ranges** (e.g., "TP53 is mutated in 30–60% of samples") rather than a single average
- **NEVER** sum mutation events across studies to compute an aggregate frequency — this can exceed 100% due to double-counting
- Warn users that samples may overlap across cohorts (e.g., MSK studies may share patients)
- **Choose and state the counting unit**: use patient-level frequencies for prevalence/rate questions unless the user explicitly asks for samples; use sample-level frequencies when the user asks about samples.
- **For "across cancer types" questions**, jump to the [Cross-Cancer-Type Mutation Frequency](#cross-cancer-type-mutation-frequency) section below — there is one correct recipe and several common wrong ones.

## Counting Unit: Samples vs Patients

Before answering any mutation count or frequency question, decide whether the unit is samples or patients and state that choice in the answer.

| User wording | Counting unit |
|--------------|---------------|
| "prevalence", "rate", "fraction of patients", "patients with", "how common is" | Patient-level: `COUNT(DISTINCT patient_unique_id)` |
| "samples", "specimens", "biopsies", sample-level cohort composition | Sample-level: `COUNT(DISTINCT sample_unique_id)` |
| Ambiguous | Ask, or default to patient-level for prevalence/rate language and say so |

### Cross-study sample-count caveat

When an answer touches more than one study and reports a sample count, prepend a one-line caveat:

> Sample IDs are unique within cBioPortal study prefixes, not guaranteed biological-sample identifiers across studies; overlapping cohorts can count the same patient/sample more than once.

Prefer one of these safer approaches:

- Use a shipped `cancer_study_query_preferences` cohort such as `pan_cancer_tcga` or `all_studies_non_redundant`.
- Restrict to one named study.
- Aggregate by `patient_unique_id` when the biological question is patient prevalence.

## STOP rule: a frequency above 100% means your query is wrong

If your query returns a frequency over 100%, **do not try to debug or explain the data inconsistency to the user**. The cause is always one of these query bugs:

- Summing mutation events instead of `COUNT(DISTINCT sample_unique_id)` for the numerator
- Using a study-wide sample count as the denominator instead of the gene-specific profiled count
- Cross-study aggregation where the same biological sample appears under multiple `sample_unique_id` values (e.g., MSK-IMPACT and MSK-CHORD share patients)
- **Joining the profiled CTE through `gene_panel` / `gene_panel_list` without a WES branch.** `gene_panel_id = 'WES'` is *not* a row in … (35166 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT cancer_study_identifier, hugo_gene_symbol, mutation_variant, mutation_type, mutation_status, COUNT(DISTINCT sample_unique_id) AS samples
FROM genomic_event_derived
WHERE hugo_gene_symbol = 'PIK3CA'
  AND (mutation_variant LIKE '%1069%' OR mutation_variant LIKE '%X1069%' OR mutation_variant LIKE '%*1069%')
GROUP BY cancer_study_identifier, hugo_gene_symbol, mutation_variant, mutation_type, mutation_status
ORDER BY samples DESC",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"msk_impact_50k_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":3},{"cancer_study_identifier":"msk_impact_50k_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutation_type":"Frame_Shift_Ins","mutation_status":"SOMATIC","samples":3},{"cancer_study_identifier":"msk_impact_2017","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutation_type":"Frame_Shift_Ins","mutation_status":"NA","samples":3},{"cancer_study_identifier":"msk_met_2021","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"msk_met_2021","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutation_type":"Frame_Shift_Ins","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"cellline_ccle_broad","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"NA","samples":2},{"cancer_study_identifier":"ccle_broad_2025","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"NA","samples":2},{"cancer_study_identifier":"ccle_genentech_2014","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"NA","samples":2},{"cancer_study_identifier":"pancan_mimsi_msk_2024","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"ccle_broad_2019","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"NA","samples":2},{"cancer_study_identifier":"crc_msk_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"msk_chord_2024","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Wext*4","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"msk_impact_50k_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069*","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"msk_chord_2024","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutation_type":"Frame_Shift_Ins","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"breast_msk_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069*","mutation_type":"Nonstop_Mutation","mutation_status":"SOMATIC","samples":2},{"cancer_study_identifier":"breast_msk_2025","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutation_type":"Frame_Shift_Ins","mutation_status":"SOMATIC","samples":1},{"cancer_study_identifier":"mycf_msk_2026","hugo_gene_symbol":"PIK3CA","mutation_variant":"*1069Ffs*5","mutat … (4697 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT cancer_study_identifier, sample_unique_id, mutation_variant, mutation_type, mutation_status, chromosome, start_position, end_position, reference_allele, variant_allele
FROM genomic_event_derived
WHERE hugo_gene_symbol = 'PIK3CA'
  AND mutation_variant = '*1069Wext*4'
ORDER BY cancer_study_identifier",
 "max_rows": 50
}

▶ clickhouse_list_table_columns
{
 "table": "genomic_event_derived"
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression identifier `chromosome` in scope SELECT cancer_study_identifier, sample_unique_id, mutation_variant, mutation_type, mutation_status, chromosome, start_position, end_position, reference_allele, variant_allele FROM genomic_event_derived WHERE (hugo_gene_symbol = 'PIK3CA') AND (mutation_variant = '*1069Wext*4') ORDER BY cancer_study_identifier ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

◀ result
{"columns":[{"name":"sample_unique_id","type":"String"},{"name":"hugo_gene_symbol","type":"String","comment":"HUGO gene symbol (e.g., TP53, KRAS, BRAF). Use for gene-specific queries."},{"name":"entrez_gene_id","type":"Int32"},{"name":"gene_panel_stable_id","type":"LowCardinality(String)"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"genetic_profile_stable_id","type":"LowCardinality(String)"},{"name":"variant_type","type":"LowCardinality(String)","comment":"Type of genomic event: \"mutation\" for SNVs/indels, \"cna\" for copy number alterations, \"structural_variant\" for SVs. Always filter by this."},{"name":"mutation_variant","type":"String","comment":"Protein change notation (e.g., p.V600E, p.R175H). Use for specific variant queries. \"NA\" for non-mutation events."},{"name":"mutation_type","type":"LowCardinality(String)"},{"name":"mutation_status","type":"LowCardinality(String)","comment":"For mutations: Somatic, Germline, UNKNOWN, or UNCALLED. Filter mutation_status != \"UNCALLED\" to exclude uncertain calls. Include all other statuses."},{"name":"driver_filter","type":"LowCardinality(String)"},{"name":"driver_filter_annotation","type":"String"},{"name":"driver_tiers_filter","type":"LowCardinality(String)"},{"name":"driver_tiers_filter_annotation","type":"String"},{"name":"cna_alteration","type":"Nullable(Int8)","comment":"Copy number alteration: only 2 = amplification (AMP) and -2 = deep deletion (HOMDEL) are stored. Shallow deletion (-1), diploid (0) and gain (1) are not in this table; query genetic_alteration_derived WHERE profile_type = 'gistic' (alteration_value is a String, e.g. '-1'). NULL for non-CNA events."},{"name":"cna_cytoband","type":"String"},{"name":"sv_event_info","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"off_panel","type":"Bool","comment":"Boolean: 1 = mutation outside gene panel coverage (off-panel), 0 = within panel (on-panel). Filter off_panel = 0 for reliable frequency calculations."}]}

▶ clickhouse_run_select_query
{
 "query": "SELECT g.cancer_study_identifier, g.sample_unique_id, g.mutation_status, g.driver_filter, g.driver_filter_annotation, g.off_panel,
       (SELECT attribute_value FROM clinical_data_derived cd WHERE cd.sample_unique_id = g.sample_unique_id AND cd.attribute_name = 'CANCER_TYPE' LIMIT 1) AS cancer_type
FROM genomic_event_derived g
WHERE g.hugo_gene_symbol = 'PIK3CA'
  AND g.mutation_variant = '*1069Wext*4'
ORDER BY g.cancer_study_identifier",
 "max_rows": 50
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 1\n Code: 1. DB::Exception: Resolved identifier 'g.sample_unique_id' in parent scope to expression 'g.sample_unique_id' with correlated columns 'sample_unique_id' (Enable 'allow_experimental_correlated_subqueries' setting to allow correlated subqueries execution). In scope (SELECT attribute_value FROM clinical_data_derived AS cd WHERE (cd.sample_unique_id = g.sample_unique_id) AND (cd.attribute_name = 'CANCER_TYPE') LIMIT 1) AS cancer_type. (UNSUPPORTED_METHOD) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "SELECT g.cancer_study_identifier, g.sample_unique_id, g.mutation_status, g.driver_filter, g.driver_filter_annotation, g.off_panel,
       cd.attribute_value AS cancer_type
FROM genomic_event_derived g
LEFT JOIN clinical_data_derived cd
  ON cd.sample_unique_id = g.sample_unique_id AND cd.attribute_name = 'CANCER_TYPE'
WHERE g.hugo_gene_symbol = 'PIK3CA'
  AND g.mutation_variant = '*1069Wext*4'
ORDER BY g.cancer_study_identifier",
 "max_rows": 50
}

◀ result
{"rows":[{"cancer_study_identifier":"brca_metabric","sample_unique_id":"brca_metabric_MB-4959","mutation_status":"NA","off_panel":false,"cancer_type":"Breast Cancer"},{"cancer_study_identifier":"ccle_broad_2019","sample_unique_id":"ccle_broad_2019_IGROV1_OVARY","mutation_status":"NA","off_panel":false,"cancer_type":"Ovarian Cancer"},{"cancer_study_identifier":"ccle_broad_2019","sample_unique_id":"ccle_broad_2019_KYSE70_OESOPHAGUS","mutation_status":"NA","off_panel":false,"cancer_type":"Esophagogastric Cancer"},{"cancer_study_identifier":"ccle_broad_2025","sample_unique_id":"ccle_broad_2025_IGROV1_OVARY","mutation_status":"NA","off_panel":false,"cancer_type":"Ovarian Cancer"},{"cancer_study_identifier":"ccle_broad_2025","sample_unique_id":"ccle_broad_2025_KYSE70_OESOPHAGUS","mutation_status":"NA","off_panel":false,"cancer_type":"Esophagogastric Cancer"},{"cancer_study_identifier":"ccle_genentech_2014","sample_unique_id":"ccle_genentech_2014_S-IGROV-1","mutation_status":"NA","off_panel":false,"cancer_type":"Ovarian Cancer"},{"cancer_study_identifier":"ccle_genentech_2014","sample_unique_id":"ccle_genentech_2014_S-KYSE-70","mutation_status":"NA","off_panel":false,"cancer_type":"Esophagogastric Cancer"},{"cancer_study_identifier":"cellline_ccle_broad","sample_unique_id":"cellline_ccle_broad_IGROV1_OVARY","mutation_status":"NA","off_panel":false,"cancer_type":"Ovarian Cancer"},{"cancer_study_identifier":"cellline_ccle_broad","sample_unique_id":"cellline_ccle_broad_KYSE70_OESOPHAGUS","mutation_status":"NA","off_panel":false,"cancer_type":"Esophagogastric Cancer"},{"cancer_study_identifier":"cellline_nci60","sample_unique_id":"cellline_nci60_IGROV1","mutation_status":"NA","off_panel":false,"cancer_type":"Ovarian Cancer"},{"cancer_study_identifier":"coadread_dfci_2016","sample_unique_id":"coadread_dfci_2016_coadread_dfci_2016_1762","mutation_status":"NA","off_panel":false,"cancer_type":"Colorectal Cancer"},{"cancer_study_identifier":"crc_msk_2026","sample_unique_id":"crc_msk_2026_P-0038429-T01-IM6","mutation_status":"SOMATIC","off_panel":false,"cancer_type":"Colorectal Cancer"},{"cancer_study_identifier":"crc_msk_2026","sample_unique_id":"crc_msk_2026_P-0077592-T01-IM7","mutation_status":"SOMATIC","off_panel":false,"cancer_type":"Colorectal Cancer"},{"cancer_study_identifier":"gbm_tcga","sample_unique_id":"gbm_tcga_TCGA-32-1979-01","mutation_status":"Somatic","off_panel":false,"cancer_type":"Glioma"},{"cancer_study_identifier":"gbm_tcga_gdc","sample_unique_id":"gbm_tcga_gdc_TCGA-32-1979-01","mutation_status":"Somatic","off_panel":false,"cancer_type":"Glioblastoma Multiforme"},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018","sample_unique_id":"gbm_tcga_pan_can_atlas_2018_TCGA-32-1979-01","mutation_status":".","off_panel":false,"cancer_type":"Glioblastoma"},{"cancer_study_identifier":"gbm_tcga_pub2013","sample_unique_id":"gbm_tcga_pub2013_TCGA-32-1979-01","mutation_status":"Unknown","off_panel":false,"cancer_type":"Glioma"},{"cancer_study_identifi … (1802 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT DISTINCT driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation
FROM genomic_event_derived
WHERE hugo_gene_symbol = 'PIK3CA' AND mutation_variant = '*1069Wext*4'"
}

◀ result
{"rows":[{}]}

▶ resolve_and_route
{
 "studyIds": [
  "msk_chord_2024",
  "gbm_tcga_pan_can_atlas_2018"
 ]
}

◀ result
{"success":true,"message":"Found 2 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":2,"studiesWithMetadata":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040,"studyViewUrl":"https://www.cbioportal.org/study?id=msk_chord_2024","metadata":{"clinicalAttributeIds":["ADRENAL_GLANDS","BONE","CANCER_TYPE","CANCER_TYPE_DETAILED","CLINICAL_GROUP","CLINICAL_SUMMARY","CNS_BRAIN","CURRENT_AGE_DEID","DIAGNOSIS_DESCRIPTION","ETHNICITY","FRACTION_GENOME_ALTERED","GENDER","GENE_PANEL","GLEASON_FIRST_REPORTED","GLEASON_HIGHEST_REPORTED","GLEASON_SAMPLE_LEVEL","HER2","HISTORY_OF_PDL1","HR","ICD_O_HISTOLOGY_DESCRIPTION","INTRA_ABDOMINAL","LIVER","LUNG","LYMPH_NODES","METASTATIC_SITE","MSI_COMMENT","MSI_SCORE","MSI_TYPE","MUTATION_COUNT","NUM_ICDO_DX","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER","PATHOLOGICAL_GROUP","PDL1_POSITIVE","PLEURA","PRIMARY_SITE","PRIOR_MED_TO_MSK","RACE","REPRODUCTIVE_ORGANS","SAMPLE_CLASS","SAMPLE_COUNT","SAMPLE_COVERAGE","SAMPLE_TYPE","SMOKING_PREDICTIONS_3_CLASSES","SOMATIC_STATUS","STAGE_HIGHEST_RECORDED","TMB_NONSYNONYMOUS","TUMOR_PURITY"],"molecularProfileIds":["msk_chord_2024_cna","msk_chord_2024_mutations","msk_chord_2024_structural_variants"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations"]}},{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","ANEUPLOIDY_SCORE","BUFFA_HYPOXIA_SCORE","CANCER_TYPE","CANCER_TYPE_ACRONYM","CANCER_TYPE_DETAILED","DAYS_LAST_FOLLOWUP","DAYS_TO_BIRTH","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DFS_MONTHS","DFS_STATUS","DSS_MONTHS","DSS_STATUS","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GENETIC_ANCESTRY_LABEL","GRADE","HISTORY_NEOADJUVANT_TRTYN","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","IN_PANCANPATHWAYS_FREEZE","MSI_SCORE_MANTIS","MSI_SENSOR_SCORE","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_PATIENT_ID","PATH_M_STAGE","PATH_N_STAGE","PATH_T_STAGE","PERSON_NEOPLASM_CANCER_STATUS","PFS_MONTHS","PFS_STATUS","PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT","PRIOR_DX","RACE","RADIATION_THERAPY","RAGNUM_HYPOXIA_SCORE","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SUBTYPE","TBL_SCORE","TISSUE_PROSPECTIVE_COLLECTION_INDICATOR","TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR","TISSUE_SOURCE_SITE","TISSUE_SOURCE_SITE_CODE","TMB_NONSYNONYMOUS","TUMOR_TISSUE_SITE","TUMOR_TYPE","WEIGHT","WINTER_HYPOXIA_SCORE"],"molecularProfileIds":["gbm_tcga_pan_can_atlas_2018_gistic","gbm_tcga_pan_can_atlas_2018_log2CNA","gbm_tcga_pan_can … (948 more chars)

▶ navigate_to_results_view
{
 "studyIds": [
  "msk_chord_2024"
 ],
 "genes": [
  "PIK3CA: MUT=*1069Wext*4"
 ],
 "tab": "mutations"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/mutations?cancer_study_list=msk_chord_2024&gene_list=PIK3CA%3A+MUT%3D*1069Wext*4&case_set_id=msk_chord_2024_all","url":"https://www.cbioportal.org/results/mutations?cancer_study_list=msk_chord_2024&gene_list=PIK3CA%3A+MUT%3D*1069Wext*4&case_set_id=msk_chord_2024_all","data":{"studyIds":["msk_chord_2024"],"studies":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040}],"genes":["PIK3CA"],"caseSetId":"msk_chord_2024_all","pageDescription":"Detailed mutation table with lollipop plot showing mutation positions, types, and frequencies for queried genes."}}

▶ navigate_to_results_view
{
 "studyIds": [
  "gbm_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "PIK3CA"
 ],
 "tab": "mutations"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/mutations?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=PIK3CA&case_set_id=gbm_tcga_pan_can_atlas_2018_all","url":"https://www.cbioportal.org/results/mutations?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=PIK3CA&case_set_id=gbm_tcga_pan_can_atlas_2018_all","data":{"studyIds":["gbm_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sampleCount":592}],"genes":["PIK3CA"],"caseSetId":"gbm_tcga_pan_can_atlas_2018_all","pageDescription":"Detailed mutation table with lollipop plot showing mutation positions, types, and frequencies for queried genes."}}

═ answer (success)
Here are direct links to view this variant's context in cBioPortal's Mutations tab (lollipop plot, per-sample detail, and — where available — OncoKB annotation live from the frontend):

**[PIK3CA \*1069Wext\*4 in MSK-CHORD (25,040 samples)](https://www.cbioportal.org/results/mutations?cancer_study_list=msk_chord_2024&gene_list=PIK3CA%3A+MUT%3D*1069Wext*4&case_set_id=msk_chord_2024_all)**
Detailed mutation table with lollipop plot showing mutation positions, types, and frequencies for queried genes.

**[PIK3CA mutations in TCGA GBM PanCancer Atlas (592 samples, includes the TCGA-32-1979 case)](https://www.cbioportal.org/results/mutations?cancer_study_list=gbm_tcga_pan_can_atlas_2018&gene_list=PIK3CA&case_set_id=gbm_tcga_pan_can_atlas_2018_all)**
Detailed mutation table with lollipop plot showing mutation positions, types, and frequencies for queried genes.

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**Bottom line:** Please verify the exact extension length (`ext*3` vs. `ext*4`) against your report's raw HGVS/genomic coordinates — this database only contains `*1069Wext*4`, a rare nonstop mutation found in <30 samples across the whole portal, with no oncogenicity/driver annotation on file here. I cannot make a clinical or functional-significance determination; the Mutations tab links above will show any live OncoKB annotation the frontend service provides.