Confirmed germline pathogenic / likely-pathogenic variant in the BAP1 gene — BAP1 tumor p...

Deterministic view of the source YAML entity. Clinical authority remains with the cited source IDs and reviewer sign-off state.

ID	`RF-BAP1-CONFIRMED-CARRIER`
Type	Red flag
Status	reviewed 2026-05-18 \| pending_clinical_signoff
Diseases	`DIS-MELANOMA` `DIS-MESOTHELIOMA` `DIS-RCC`
Sources	`SRC-ASCO-ACMG-LYNCH-2014` `SRC-NCCN-BCELL-2025`

Red Flag Origin

Definition	Confirmed germline pathogenic / likely-pathogenic variant in the BAP1 gene — BAP1 tumor predisposition syndrome (BAP1-TPDS). Patient has had germline BAP1 testing returned positive; the pedigree-suspicion question is settled. No current personal cancer diagnosis in the carrier being assessed. Mandates structured surveillance for the BAP1-spectrum cancers: uveal melanoma, cutaneous melanoma, malignant mesothelioma (pleural + peritoneal), clear-cell RCC, and atypical Spitz tumors (often as childhood / adolescent sentinels). Prevention- persona RedFlag (§20, v0.2-B confirmed-carrier surveillance pathway — distinct from RF-BAP1-FAMILY-HISTORY-SUSPICION which fires before testing).
Clinical direction	investigate
Category	other

Trigger Logic

{
  "any_of": [
    {
      "finding": "germline_bap1_pathogenic_variant_confirmed",
      "value": true
    }
  ],
  "type": "lab_value"
}

Notes

v0.2-B confirmed-carrier surveillance pathway — BAP1-TPDS. Fires on documented germline BAP1 pathogenic variant positivity. Engine routes to PreventionPlan recommending: (a) IND-BAP1-CARRIER-SURVEILLANCE (standard) — annual whole-body skin exam by dermatologist; annual ophthalmologic exam with dilated fundoscopy for uveal melanoma; annual abdominal MRI for clear-cell RCC; chest CT q1-3y for mesothelioma surveillance; explicit awareness of atypical Spitz tumors as sentinel lesions. (b) IND-BAP1-CARRIER-INTENSIFIED (aggressive) — standard PLUS asbestos-avoidance counseling (most important modifiable cofactor for BAP1-associated mesothelioma) + earlier mesothelioma surveillance (chest CT q1y in occupational / environmental asbestos exposure). STUB pending two-Clinical-Co-Lead signoff per CHARTER §6.1 dev-mode exemption. Source-set TODO: dedicated BAP1-TPDS sources — Pilarski et al. surveillance recommendations (J Med Genet 2020); Carbone et al. mechanistic + clinical reviews — v0.2-B authoring backlog new SRC entities. Lifetime cancer risk in confirmed BAP1 carriers (Pilarski J Med Genet 2020; Walpole et al. JNCI 2018): - Uveal melanoma: ~25-30% lifetime — BAP1-TPDS is the only major...

Used By

Indications

IND-BAP1-CARRIER-INTENSIFIED - IND-BAP1-CARRIER-INTENSIFIED
IND-BAP1-CARRIER-SURVEILLANCE - IND-BAP1-CARRIER-SURVEILLANCE
IND-FAMMM-CARRIER-SURVEILLANCE - IND-FAMMM-CARRIER-SURVEILLANCE