Stage II: Summary Report Secondary Findings in Adults Non-diagnostic, excludes newborn screening & prenatal testing/screening Stage I Survey Update History Stage 2 Status (Adult):Complete (Actionability curation complete.)

GENE/GENE PANEL: BAP1
Condition: Tumor Predisposition Syndrome
GENEDISEASE PAIRS: BAP1614327
Topic
Narrative Description of Evidence
Ref
1. What is the nature of the threat to health for an individual carrying a deleterious allele?
Prevalence of the Genetic Disorder
The population prevalence of BAP1 tumor predisposition syndrome (BAP1-TPDS) is unknown, though estimated to be rare. A 2015 review identified 57 published families with 174 individuals with BAP-TPDS. The prevalence of germline mutations in individuals with BAP1 associated cancers include: uveal melanoma (1-3%), malignant mesothelioma (6%), and cutaneous melanoma (0.6%). The prevalence of BAP1-TPDS in persons with other cancers is unknown.
1 2 3 4
Clinical Features
(Signs / symptoms)
BAP1-TPDS is characterized by heterozygous pathogenic variants in the BAP1 gene, resulting in haploinsufficiency of the putative tumor suppressor protein BAP1. Tumors develop from cell types in which loss of heterozygosity occurs. Atypical Spitz tumors (ASTs), a specific type of skin lesion, may be the most common manifestation of BAP1-TPDS. These lesions are skin-colored to reddish brown, average 5 mm in diameter, and are histologically between those of a Spitz nevus and melanoma. In addition to ASTs, patients are at increased risk for certain malignancies. Individuals with pathogenic BAP1 mutations are prone to develop uveal melanoma, malignant mesothelioma, cutaneous melanoma, clear cell renal cell carcinoma (ccRCC), and basal cell carcinoma. Affected individuals can have more than one type of primary cancer. Other cancers with some, but inconsistent, evidence for their inclusion in the spectrum of BAP1-TPDS malignancies are breast cancer, cholangiocarcinoma, meningioma, neuroendocrine tumors, non-small cell lung adenocarcinoma, and thyroid cancer.
1 2 5 6 7
Natural History
(Important subgroups & survival / recovery)
Patients are reported to develop ASTs as early as the second decade of life, and for some patients these may be the first presenting symptom. However, patients have been found to have a low number of melanomas compared to the number of atypical Spitz tumors, suggesting the risk of malignant progression in individual tumors is low. Almost all malignancies associated with BAP1-TPDS have an earlier onset than in the general population and a worse prognosis. Uveal melanoma in BAP1-TPDS has an earlier age of onset compared with the general population (51 years vs 62 years) and are typically more aggressive with a poorer prognosis (average survival of 4.74 years versus 9.97 years for persons with tumors expressing BAP1). Malignant mesothelioma occurs significantly earlier than that of sporadic malignant mesothelioma (55-58 years vs 68-72 years), with higher rates of peritoneal involvement and the majority of peritoneal cases occurring in women. In contrast to other BAP1-TPDS cancers, survival in persons with BAP1-related malignant mesothelioma may be longer than in sporadic cases, although data are not consistent. Growing evidence suggests that asbestos exposure increases the risk for mesothelioma in patients with pathogenic variants in BAP1. Cutaneous melanoma often occurs with multiple primary melanomas and has an earlier onset (46 years vs 58 years). The data regarding aggressiveness of BAP1-associated cutaneous melanoma relative to sporadic instances is inconsistent. Median age of ccRCC diagnosis is earlier than that of sporadic ccRCC (47 vs 64 years), and length of survival is also decreased with individuals generally having a higher grade of cancer at diagnosis. Based on limited data basal cell carcinoma appears to have a median age of onset at 50 years.
1 2 4 5 7
2. How effective are interventions for preventing harm?
Information on the effectiveness of the recommendations below was not provided unless otherwise stated.
Patient Management
Following diagnosis, the patient should be thoroughly evaluated for ASTs, cutaneous melanoma, and/or basal cell carcinoma, uveal melanoma, malignant mesothelioma, and clear cell renal cell carcinoma. Initial workup for cutaneous disease should include full body skin examination by a dermatologist with excision of any lesions suggestive of an AST. Initial examination for uveal melanoma should include a dilated eye examination and imaging by an ocular oncologist. For ccRCC, an abdominal ultrasound exam, urinalysis, and abdominal MRI are recommended. It is recommended that MRI evaluation of the peritoneum and pleura be considered to evaluate for malignant mesothelioma. The use of spiral chest CT is controversial due to the risk of cancer from radiation exposure. (Tier 4)
1 2
Surveillance
Yearly dilated eye examinations and imaging by an ocular oncologist are recommended for the detection of uveal melanoma. In the case of a uveal melanoma diagnosis, consider high-risk patient monitoring protocol for systemic metastatic surveillance (e.g., liver-directed imaging every 3-6 months, pulmonary imaging every 6-12 months) (Tier 4)
1 2
No data exist regarding the effectiveness of uveal melanoma surveillance or treatment in this population. Surveillance for uveal melanoma may allow detection at an earlier stage. Uveal melanomas in BAP1-TPDS are aggressive and should be managed according to standard practice for more aggressive tumors, even when detected at an earlier stage. (Tier 4)
1 2
Because tumor size and stage are correlated with prognosis and risk of metastasis in average-risk populations, it is suggestive that early diagnosis and treatment may improve outcomes. (Tier 5)
8 9 10
Individuals should undergo an annual full-body dermatology exam beginning around age 20 years. In addition, patients should perform skin self-exam following the characteristics of melanoma. (Tier 4)
1 2
No data exist regarding the effectiveness of melanoma surveillance in this population. A systematic review addressing visual screening for skin cancer identified no trials addressing the effectiveness of skin cancer screening on morbidity and mortality in average-risk individuals. One ecological study found that after the implementation of a population based skin cancer screening program the population age- and sex-adjusted melanoma mortality decreased by 48% with an absolute mortality difference of 0.8 melanoma deaths per 100,000 persons. Eight observational studies examined the association between lesion thickness or stage at diagnosis and mortality. All studies demonstrated a consistent linear increase in the risk of melanoma mortality with increasing tumor thickness. Tumor thickness >4.0mm was associated with a hazard ratio of 3.1-32.6 in multivariate models, indicating increased risk of melanoma mortality compared with thinner lesions. (Tier 5)
11
No reliable early disease symptoms or screening modalities for malignant mesothelioma exist. However, annual evaluation is recommended for the detection of late manifestations of mesothelioma (e.g., chest pain, cough, shortness of breath), signs of pleurisy (pleural inflammation), peritonitis, ascites, and/or pleural effusion. If abdominal MRI is being performed to evaluate for ccRCC, evaluation of peritoneum and pleura can be considered. Recommendation for spiral chest CT is controversial due to the risk of cancer from radiation exposure. In general, malignant mesothelioma is highly refractory to conventional therapies including surgical intervention and multimodal strategies; thus a cure is unlikely. (Tier 4)
1 2
Annual abdominal ultrasound examination is recommended along with consideration of annual urinalysis and abdominal MRI every two years for the detection of ccRCC. ccRCC in BAP1-TPDS should be managed according to standard practice. (Tier 4)
1 2
Family Management
It is appropriate to clarify the genetic status of asymptomatic older and younger (including pre-adolescents) at-risk relatives of a known affected individual by molecular genetic testing for the BAP1 pathogenic variant in the family in order to identify as early as possible those who would benefit from prompt initiation of screening and preventive measures. (Tier 4)
1 2 7
Circumstances to Avoid
Arc welding has been associated with risk of uveal melanoma and should be avoided if possible. (Tier 4)
2
Because of the increased risk for malignant mesothelioma, individuals should avoid smoking and asbestos exposure. (Tier 4)
2
Individuals should avoid unnecessary and prolonged sun exposure and utilize sun protection (sunscreen and protective clothing) due to an increased risk of melanoma and basal cell carcinoma. The use of sunglasses with high UVA and UVB protection may help reduce the risk of cancer on the eye lids, but data regarding the benefits of sunglasses for uveal melanoma are lacking. (Tier 4)
1 2
3. What is the chance that this threat will materialize?
Mode of Inheritance
Autosomal Dominant
 
Prevalence of Genetic Mutations
No data were found on the population prevalence of pathogenic germline mutations in BAP1.
 
Penetrance
OR
Relative Risk
(Include any high risk racial or ethnic subgroups)
A review of family reports from the literature found that overall 148 of 174 individuals (85%) with BAP1-TPDS had a malignant manifestation
 
- Uveal melanoma: 54/174 (31%)
 
- Malignant mesothelioma: 39/174 (22%)
 
- Cutaneous melanoma: 23/174 (13%)
 
- Renal cell carcinoma: 18/174 (10%)
 
- Cutaneous melanocytic lesions (ASTs): 31/43 (72%)
 
Potentially associated cancers:
 
- Breast cancer: 9/95 (9.5%)
 
- Basal cell carcinoma: 11/174 (6.3%)
 
It is likely, however, that these penetrance data are inflated by test bias since the patients and family members who get tested are generally those affected by cancer. Of the 57 reported families, only the affected proband was tested in 30, and only 17 families had more than 3 individuals tested. Thus, the true penetrance for BAP1 mutations may well be lower than currently estimated. (Tier 3)
1 2
No data were found regarding the relative risk of manifestations of BAP1-TPDS.
 
 
Expressivity
The type of BAP1-related tumors can vary among different members of the same family. (Tier 4)
2
4. What is the Nature of the Intervention?
Nature of Intervention
Most recommended interventions are non-invasive surveillance and thorough initial work-up and have little associated risks. If a spiral chest CT is performed to examine the patient for mesothelioma, the test carries some risk of cancer development from the radiation exposure itself.
2
5. Would the underlying risk or condition escape detection prior to harm in the settting of recommended care?
Chance to Escape Clinical Detection
Cancers associated with this condition are earlier onset and typically more aggressive than those in the general population. Because there are no standard recommendations for screenings related to these types of cancer, there is a high chance for them to escape clinical detection in the setting of recommended care. Both cutaneous melanomas and uveal melanomas can be cured when found at an early stage but are fatal upon metastasis. (Tier 4)
2 7

 
Final Consensus Scores
Outcome / Intervention Pair
Severity
Likelihood
Effectiveness
Nature of the
Intervention
Total
Score
Malignant Mesothelioma / Imaging
2
2C
0C
2
6CC
Melanoma / Annual full-body dermatology exam
2
2C
2N
3
9CN
Uveal Melanoma / Annual eye exam, including dilated eye exam, by ocular oncologist
2
2C
0C
3
7CC
Clear Cell Renal Cell Carcinoma / Abdominal Ultrasound
2
2C
3D
3
10CD
To see the scoring key, please go to: https://clinicalgenome.org/working-groups/actionability/projects-initiatives/actionability-evidence-based-summaries/
Description of sources of evidence:
Tier 1: Evidence from a systematic review, or a meta-analysis or clinical practice guideline clearly based on a systematic review.
Tier 2: Evidence from clinical practice guidelines or broad-based expert consensus with non-systematic evidence review.
Tier 3: Evidence from another source with non-systematic review of evidence with primary literature cited.
Tier 4: Evidence from another source with non-systematic review of evidence with no citations to primary data sources.
Tier 5: Evidence from a non-systematically identified source.
Reference List
1. Rai K, Pilarski R, Cebulla CM, Abdel-Rahman MH. Comprehensive review of bap1 tumor predisposition syndrome with report of two new cases. Clin Genet. (2016) 89(3):285-94.
2. R Pilarski, K Rai, C Cebulla, M Abdel-Rahman. Bap1 tumor predisposition syndrome. 2016 Oct 13. In: RA Pagon, MP Adam, HH Ardinger, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2018. Available from: http://www.ncbi.nlm.nih.gov/books/NBK390611
3. Magnani C, Bianchi C, Chellini E, Consonni D, Fubini B, Gennaro V, Marinaccio A, Menegozzo M, Mirabelli D, Merler E, Merletti F, Musti M, Oddone E, Romanelli A, Terracini B, Zona A, Zocchetti C, Alessi M, Baldassarre A, Dianzani I, Maule M, Mensi C, Silvestri S. III Italian Consensus Conference on Malignant Mesothelioma of the Pleura. Epidemiology, public health and occupational medicine related issues. Med Lav. (2015) 106(5):325-32.
4. Field MG, Harbour JW. Recent developments in prognostic and predictive testing in uveal melanoma. Curr Opin Ophthalmol. (2014) 25(3):234-9.
5. Online Medelian Inheritance in Man, OMIM®. Johns Hopkins University, Baltimore, MD. Tumor predisposition syndrome; tpds. MIM: 614327: 2013 Jul 11. World Wide Web URL: http://omim.org.
6. Online Medelian Inheritance in Man, OMIM®. Johns Hopkins University, Baltimore, MD. Brca1-associated protein 1; bap1. MIM: 603089: 2014 Jan 28. World Wide Web URL: http://omim.org.
7. Battaglia A. The importance of multidisciplinary approach in early detection of bap1 tumor predisposition syndrome: clinical management and risk assessment. Clin Med Insights Oncol. (2014) 8:37-47.
8. Damato B. Progress in the management of patients with uveal melanoma. The 2012 ashton lecture. Eye (Lond). (2012) 26(9):1157-72.
9. Weis E, Salopek TG, McKinnon JG, Larocque MP, Temple-Oberle C, Cheng T, McWhae J, Sloboda R, Shea-Budgell M. Management of uveal melanoma: a consensus-based provincial clinical practice guideline. Curr Oncol. (2016) 23(1):e57-64.
10. Krantz BA, Dave N, Komatsubara KM, Marr BP, Carvajal RD. Uveal melanoma: epidemiology, etiology, and treatment of primary disease. Clin Ophthalmol. (2017) 11:279-289.
11. Wernli KJ, Henrikson NB, Morrison CC, Nguyen M, Pocobelli G, Blasi PR. Screening for skin cancer in adults: updated evidence report and systematic review for the us preventive services task force. JAMA. (2016) 316(4):436-47.
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