Clinical characteristics.

BAP1 tumor predisposition syndrome (BAP1-TPDS) is associated with an increased risk for a specific skin lesion, BAP1-inactivated melanocytic tumors (BIMT; formerly called atypical Spitz tumors), and the following cancers, in descending order of frequency: uveal (eye) melanoma (UM), malignant mesothelioma (MMe), cutaneous melanoma (CM), renal cell carcinoma (RCC), basal cell carcinoma (BCC), meningioma, and cholangiocarcinoma. Onychopapillomas, hepatocellular carcinoma, and ovarian sex cord-stromal tumors may also be associated with BAP1-TPDS. Affected individuals can have more than one type of primary cancer. In general, the median age of onset of these tumors is younger than in the general population. UM tends to be a more aggressive class 2 tumor with higher risk for metastasis and reduced survival compared to UM occurring in the general population. RCC is usually of clear cell morphology, but other pathologies have been reported. MMe, especially pleural, has better survival and responds better to platinum chemotherapy than MMe not associated with a germline BAP1 pathogenic variant. The penetrance, natural history, life-time cancer risk for carriers, and frequencies of BAP1-associated tumors are yet to be fully determined.

Diagnosis/testing.

The diagnosis of BAP1-TPDS is established in a proband by identification of a heterozygous germline pathogenic variant in BAP1 on molecular genetic testing.

Management.

Treatment of manifestations: Treatment of CM, BCC, and RCC per established clinical guidelines. UM treatment should be the same as the more aggressive class 2 or monosomy 3 tumors because of the increased aggressiveness of BAP1-related UM. MMe treatment per oncologist familiar with BAP1-related MMe. Meningiomas are usually higher grade / atypical and should be treated accordingly. Treatment of other cancers per established clinical guidelines.

Prevention of primary manifestations: UM: avoid arc-welding. MMe: avoid asbestos exposure (including naturally occurring tremolite and erionite) and smoking. CM and BCC: limit sun exposure, use sunscreen and protective clothing, and perform regular dermatologic examinations.

Surveillance: BIMT, CM, BCC: annual full-body dermatologic examinations beginning at age 18 years; consider follow-up total body photography in those with a large number of skin lesions as needed. UM: annual dilated eye examinations beginning at age 11-18 years or at puberty with referral to ocular oncologist for any pigmented lesions. MMe, RCC: annual clinical evaluation for manifestations of pleurisy, peritonitis, ascites, and/or pleural effusion and RCC beginning at age 30 years; renal/abdominal and chest ultrasound every two years alternating with abdominal and chest MRI every two years beginning at age 30 years.

Agents/circumstances to avoid: Arc welding, asbestos including naturally occurring tremolite and erionite, smoking, unnecessary and prolonged sun exposure, routine chest radiographs, and CT examinations.

Evaluation of relatives at risk: It is appropriate to clarify the genetic status of at-risk relatives 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 surveillance and counseling regarding agents/circumstances to avoid.

Genetic counseling.

BAP1-TPDS is inherited in an autosomal dominant manner. Most individuals diagnosed with BAP1-TPDS have an affected parent (an affected parent may have BAP1-related tumors that differ from those of the proband). Some individuals have BAP1-TPDS as the result of a de novo pathogenic variant. Each child of an individual with BAP1-TPDS has a 50% chance of inheriting the BAP1 pathogenic variant. Once a germline BAP1 pathogenic variant has been identified in an affected family member, predictive testing for at-risk family members and prenatal and preimplantation genetic testing are possible.

Suggestive Findings

BAP1-TPDS should be suspected in probands with EITHER of the following:

• Two or more confirmed BAP1-TPDS tumors *
• One BAP1-TPDS tumor and a first- or second-degree relative with a confirmed BAP1-TPDS tumor *

* Excluding two basal cell cancers and/or cutaneous melanomas, given their high frequency in the general population

Confirmed BAP1-TPDS tumors include the following (in descending order of likelihood):

• BAP1-inactivated melanocytic tumors (BIMT). Formerly called atypical Spitz tumors, these may be the most common manifestation of BAP1-TPDS and may result in the initial identification of a proband. BIMT are skin colored to reddish brown, averaging 5 mm in diameter; the histologic findings are between those of a Spitz nevus and a melanoma. Both copies of BAP1 are inactivated, leading to loss of staining for the BAP1 protein on immunohistochemistry; in addition, BIMT usually have the somatic BRAF pathogenic variant p.Val600Glu.
• Uveal (eye) melanoma (UM)
• Malignant mesothelioma (MMe)
• Cutaneous melanoma (CM)
• Renal cell carcinoma (RCC)
• Basal cell carcinoma (BCC), meningioma, and cholangiocarcinoma, which appear to be less common manifestations of BAP1-TPDS

Unconfirmed tumors include the following (in alphabetic order):

• Breast cancer
• Colon polyps and colon cancer
• Hepatocellular carcinoma
• Neuroendocrine tumors
• Non-small cell lung adenocarcinoma
• Onychopapilloma
• Ovarian sex cord-stromal tumors
• Thyroid cancer
• Urinary bladder cancer

Establishing the Diagnosis

The diagnosis of BAP1-TPDS is established in a proband by identification of a heterozygous germline pathogenic (or likely pathogenic) variant in BAP1 on molecular genetic testing (see Table 1).

Note: (1) Per ACMG/AMP variant interpretation guidelines, the terms "pathogenic variant" and "likely pathogenic variant" are synonymous in a clinical setting, meaning that both are considered diagnostic and can be used for clinical decision making [Richards et al 2015]. Reference to "pathogenic variants" in this GeneReview is understood to include likely pathogenic variants. (2) Identification of a heterozygous BAP1 variant of uncertain significance does not establish or rule out the diagnosis.

Molecular genetic testing approaches can include single gene testing or use of a multigene panel:

• Single-gene testing. Sequence analysis of BAP1 is performed first to detect missense, nonsense, and splice site variants and small intragenic deletions/insertions. Note: Depending on the sequencing method used, single-exon, multiexon, or whole-gene deletions/duplications may not be detected. If no variant is detected by the sequencing method used, the next step is to perform gene-targeted deletion/duplication analysis to detect exon and whole-gene deletions or duplications.
• A cancer predisposition multigene panel that includes BAP1 and other genes of interest (see Differential Diagnosis) may also be considered to identify the genetic cause of the condition while limiting identification of variants of uncertain significance and pathogenic variants in genes that do not explain the underlying phenotype. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests.
  For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.

Clinical Description

BAP1 tumor predisposition syndrome (BAP1-TPDS) is associated with increased risk for a specific skin lesion, BAP1-inactivated melanocytic tumor (BIMT; formerly called atypical Spitz tumor), and several cancers including uveal (eye) melanoma (UM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), cutaneous melanoma (CM), basal cell carcinoma (BCC), meningioma, and cholangiocarcinoma. Affected individuals can have more than one type of primary cancer [Abdel-Rahman et al 2011, Testa et al 2011, Wiesner et al 2011, Popova et al 2013, Walpole et al 2018]. Because of the limited number of families reported to date and the ascertainment bias of research groups focusing on UM, MMe, and CM, the penetrance and frequencies of the various BAP1-associated tumors are yet to be determined. To adjust for ascertainment bias, Walpole et al [2018] compared the prevalence of each component tumor in probands with BAP1-TPDS to the prevalence in relatives known to also have a BAP1 pathogenic variant. The following is a summary of the evidence for the association of different tumors with BAP1-TPDS [Strande et al 2017].

Genotype-Phenotype Correlations

Some BAP1 missense pathogenic variants have been reported to be associated with Kury-Isidor syndrome (see Genetically Related Disorders) [Küry et al 2022].

BAP1 pathogenic variants associated with BAP1-TPDS are mostly loss-of-function variants. Several missense variants have been reported in individuals presenting with BAP1-TPDS. As of November 19, 2024, there are eight missense variants (including seven in the BAP1 ubiquitin carboxyl-terminal hydrolase domain) that have been reported as pathogenic / likely pathogenic in ClinVar. Some of these variants segregate with the BAP1 associated cancers in the family.

Penetrance

The penetrance of BAP1-TPDS appears to be high based on the published literature, with 88% of probands and 82.5% of relatives with a heterozygous germline BAP1 pathogenic variant having had a cancer diagnosis. However, ascertainment biases in favor of both testing and reporting affected versus unaffected individuals may have inflated this figure. For example, in more than half of the reported families only the proband had been tested. Also, the majority of the study participants were ascertained based on their strong family history of cancer. Given these biases, an accurate estimate of penetrance cannot be determined at this time. In attempting to adjust for this, Walpole et al [2018] found a significantly lower prevalence of BAP1-related tumors in affected relatives compared to probands (see Prevalence).

Nomenclature

BAP1-inactivated melanocytic tumors have also been called the following:

• Atypical Spitz tumors
• Nevoid melanoma-like melanocytic proliferations (NEMMP) [Njauw et al 2012]
• Melanocytic BAP1-mutated atypical intradermal tumors (MBAITS) [Carbone et al 2012]
• BAPoma

Prevalence

The prevalence of BAP1-TPDS is unknown. Based on data from the Genome Aggregation Database (gnomAD), the frequency of a heterozygous BAP1 pathogenic variant is 1:26,837 in the general population. In the cancer cohort from the TCGA, the frequency was 8:10,389 (1:1,299).

The prevalence of BAP1-TPDS ranges from about 10%-12% in individuals with BIMT, 1%-2% in persons with UM,1%-3% in persons with MMe [Huang et al 2018, Panou et al 2018], 0.3%-1.5% in those with RCC [Carlo et al 2018, Wu et al 2019, Han et al 2024], and 0.5% in persons with HCC [Huang et al 2018]. Several large studies showed that BAP1-TPDS is rare in those with CM (0.1%) [Aoude et al 2015, O'Shea et al 2017, Huang et al 2018]. The prevalence of BAP1-TPDS in persons with other cancers is unknown.

UM. The prevalence of germline BAP1 pathogenic variants in unselected individuals with UM is 1%-2% [Aoude et al 2013a, Gupta et al 2015, Repo et al 2019]; in contrast, the frequency is 20%-30% in persons with UM who have a family history of UM [Turunen et al 2016, Rai et al 2017]. In individuals with UM and a somatic BAP1 pathogenic variant on tumor tissue testing, the frequency of a germline BAP1 pathogenic variant is estimated to be ~2%-5%; about 40% of UM tumors have a somatic BAP1 pathogenic variant.

MMe. Germline BAP1 pathogenic variants have been identified in 1%-3% of simplex cases and 6%-7.7% (9:153) of individuals with familial MMe [Betti et al 2015, Ohar et al 2016, Betti et al 2018]. In individuals with a somatic BAP1 pathogenic variant identified on tumor tissue testing, the frequency of a germline BAP1 pathogenic variant is estimated to be ~2%-5%; about 40%-60% of MMe have a somatic BAP1 pathogenic variant.

CM. Germline BAP1 pathogenic variants were observed rarely in two large studies of sporadic CM, with a prevalence of 3:1,197 (0.25%) and 0:1,109 [Aoude et al 2015, O'Shea et al 2017]. Also, germline BAP1 pathogenic variants are rare in familial CM (0%-0.7%), particularly in those with no other cancers observed in the family [Njauw et al 2012, Boru et al 2019, Potjer et al 2019]. Given the rarity of somatic BAP1 pathogenic variants in CM, reflex germline testing is recommended in individuals with a BAP1 pathogenic variant identified on tumor tissue testing.

RCC. The frequency of a germline BAP1 pathogenic variant in unselected individuals with RCC ranges between 0.3% and 1.5%, with the highest frequency in those with clear cell subtype [Carlo et al 2018; Wu et al 2019; Han et al 2024; M Carlo et al, unpublished data]. The frequency of somatic BAP1 pathogenic variants in RCC is about 10%-15%; therefore, germline reflex testing of individuals with RCC and a BAP1 variant detected on tumor tissue testing should be considered.

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with BAP1-TPDS, the evaluations summarized in Table 3 (if not performed as part of the evaluation that led to the diagnosis) are recommended.

Treatment of Manifestations

Supportive care to improve quality of life, maximize function, and reduce complications is recommended. This ideally involves multidisciplinary care by specialists in relevant fields (see Table 4).

Prevention of Primary Manifestations

Uveal melanoma (UM). Arc welding has been associated with increased risk of UM and should be avoided if possible.

Sunglasses with high UVA and UVB protection can reduce risk of cancer on the eyelids, but data regarding the benefit of sunglasses for UM are lacking.

Malignant mesothelioma. As with all individuals, asbestos exposure (including naturally occurring tremolite and erionite) and smoking should be avoided.

Cutaneous melanoma (CM). Primary prevention is limited to those measures typically used to reduce the risk for CM, including limiting sun exposure, regular use of sunscreen and protective clothing, and regular dermatologic examinations.

Surveillance

To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, international consensus recommendations for surveillance have not been established; however, several groups have proposed variations of the recommendations summarized in Table 5) [Carbone et al 2012, Battaglia 2014, Rai et al 2016, Star et al 2018, Lalloo et al 2023].

Agents/Circumstances to Avoid

Avoid the following:

• Arc welding
• Asbestos (including naturally occurring tremolite and erionite)
• Smoking
• Unnecessary and prolonged sun exposure
• Routine chest radiographs and CT examinations

Evaluation of Relatives at Risk

It is appropriate to clarify the genetic status of apparently asymptomatic at-risk relatives of an affected individual by molecular genetic testing for the BAP1 pathogenic variant in the family. Family members who have a BAP1 pathogenic variant should be offered regular lifelong surveillance and counseled regarding agents/circumstances to avoid. Family members who have not inherited the pathogenic variant and their subsequent offspring have cancer risks similar to the general population.

Predictive genetic testing for a known familial pathogenic variant in BAP1 should be offered prior to the age that BAP1-TPDS surveillance commences (see Table 5). Note: In families with multiple cancers that cannot be explained by BAP1 alone, additional testing using an appropriate cancer panel consistent with the clinical phenotype in the family is recommended.

Note: If at-risk first-degree relatives are not able to (or choose not to) undergo molecular genetic testing for a known familial BAP1 pathogenic variant, surveillance is recommended (see Table 5) unless/until genetic testing confirms that they did not inherit the familial variant. However, in health care systems outside the United States, the surveillance protocols will be on a case-by-case basis until genetic diagnosis is confirmed.

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Therapies Under Investigation

Currently no open treatment trials specifically target individuals with BAP1-TPDS, but several trials are currently open for individuals with somatic BAP1 pathogenic variants, including PARP inhibitor therapies as single or combination therapies.

One National Cancer Institute (NCI)-sponsored trial (NCT01587352) using vorinostat in the treatment of metastatic UM is assessing BAP1 mutation status as a secondary outcome measure.

Another NCI Phase II study is currently investigating the rate of stabilization or disease improvement from investigational decitabine/cedazuridine (INQOVI) treatment in individuals with BAP1-TPDS and subclinical, early-stage mesothelioma (NCT05960773).

One study undertook saturation genome editing (SGE) of BAP1 to experimentally characterize all single-nucleotide variants in the BAP1 coding sequence; the phenome-wide association study demonstrated that disruptive germline BAP1 variants were significantly associated with higher circulating levels of the tumor promoter and mitogen insulin-like growth factor (IGF-1), suggesting a possible therapeutically targetable mechanism [Waters et al 2024].

Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions.

Mode of Inheritance

BAP1 tumor predisposition syndrome (BAP1-TPDS) is inherited in an autosomal dominant manner.

Risk to Family Members

Parents of a proband

• To date, most individuals diagnosed with BAP1-TPDS have an affected parent. An affected parent may have BAP1-related tumors that differ from those of the proband.
• Some individuals diagnosed with BAP1-TPDS have the disorder as the result of a de novo germline BAP1 pathogenic variant. In one study, two of 21 probands had BAP1-TPDS as the result of a de novo pathogenic variant [Chau et al 2019].
• If the proband appears to be the only affected family member (i.e., a simplex case), molecular genetic testing is recommended for the parents of the proband to evaluate their genetic status, inform recurrence risk assessment, and determine their need for BAP1-related cancer surveillance.
• If the germline BAP1 pathogenic variant identified in the proband is not identified in either parent and parental identity testing has confirmed biological maternity and paternity, the following possibilities should be considered:
  • The proband has a de novo pathogenic variant.
  • The proband inherited a pathogenic variant from a parent with gonadal (or somatic and gonadal) mosaicism. Note: Testing of parental leukocyte DNA may not detect all instances of somatic mosaicism and will not detect a pathogenic variant that is present in the germ (gonadal) cells only.
• The family history of some individuals diagnosed with BAP1-TPDS may appear to be negative because of failure to recognize the disorder in family members, reduced penetrance, early death of the parent before the onset of symptoms, or late onset of the disease in the affected parent. Therefore, an apparently negative family history cannot be confirmed unless molecular genetic testing has confirmed that neither of the parents has the germline BAP1 pathogenic variant identified in the proband.

Sibs of a proband. The risk to the sibs of the proband depends on the genetic status of the proband's parents:

• If a parent of the proband has the germline BAP1 pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%.
  • An accurate estimate of penetrance in heterozygous individuals cannot be determined at this time (see Penetrance).
  • The types of BAP1-related tumors can vary among affected family members.
• If the BAP1 pathogenic variant found in the proband cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is estimated to be 1% because of the possibility of parental gonadal mosaicism [Rahbari et al 2016].
• If the parents have not been tested for the BAP1 pathogenic variant but are clinically unaffected, sibs are still presumed to be at increased risk for BAP1-TPDS because of the possibility of reduced penetrance in a heterozygous parent and the possibility of parental gonadal mosaicism.

Offspring of a proband. Each child of an individual with BAP1-TPDS has a 50% chance of inheriting the BAP1 pathogenic variant.

Other family members. The risk to other family members depends on the genetic status of the proband's parents: if a parent has the germline BAP1 pathogenic variant, the parent's family members may be at risk.

Related Genetic Counseling Issues

See Management, Evaluation of Relatives at Risk for information on evaluating at-risk relatives for the purpose of early diagnosis and treatment.

Predictive testing for at-risk asymptomatic family members requires prior identification of the germline BAP1 pathogenic variant in the family.

Genetic cancer risk assessment and counseling. For a comprehensive description of the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without molecular genetic testing, see Cancer Genetics Risk Assessment and Counseling – Health Professional Version (part of PDQ^®, National Cancer Institute).

Family planning

• The optimal time for determination of genetic risk and discussion of the availability of prenatal/preimplantation genetic testing is before pregnancy.
• It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to young adults who are affected or at risk.

Prenatal Testing and Preimplantation Genetic Testing

Once a germline BAP1 pathogenic variant has been identified in an affected family member, prenatal and preimplantation genetic testing for BAP1-TPDS are possible.

Differences in perspective may exist among medical professionals and within families regarding the use of prenatal and preimplantation genetic testing. While most health care professionals would consider use of prenatal and preimplantation genetic testing to be a personal decision, discussion of these issues may be helpful.

Molecular Pathogenesis

BAP1 encodes ubiquitin carboxyl-terminal hydrolase BAP1 (BAP1). BAP1 is a nuclear-localized deubiquitinating enzyme and acts as a chromatin-associated protein that is part of large multiprotein complexes that both positively and negatively regulate cellular proliferation (reviewed in Daou et al [2015]). It is recruited to promoter regions of genes involved in cellular proliferation to activate transcription and to promote repair at sites of DNA double-strand breaks through homologous recombination [Daou et al 2015]. BAP1 cytoplasmic function is thought to be important in apoptosis [Bononi et al 2017].

Mechanism of disease causation. Loss of function. A pathogenic variant in one BAP1 allele results in haploinsufficiency of BAP1, a tumor suppressor protein. Tumors develop when the second allele acquires a second pathogenic variant, resulting in complete loss of BAP1 tumor suppressor activity. Most BAP1-inactivated melanocytic tumors analyzed by Wiesner et al [2012] showed loss of the remaining normal BAP1 allele by various somatic alterations and all showed loss of BAP1 protein in the nucleus.

Author Notes

Authors' website

The research of Dr Abdel-Rahman and Dr Cebulla is focused on identifying and characterizing hereditary causes of uveal melanoma. They were one of three groups coreporting on the identification of BAP1 tumor predisposition syndrome (BAP1-TPDS). They offer research analysis of BAP1 in families with histories suggestive of BAP1-TPDS and perform exome and other analyses on high-risk UM families without identifiable genetic causes. They currently have a clinical trial to study the frequency and clinical phenotype of BAP1 hereditary predisposition syndrome (NCT04792463). To discuss enrolling a patient please contact ude.cmuso@enryb.yesdnil.

Dr Carlo's research is on the genetics of renal cancer.

Dr Hanson is the lead author of the manuscript on the European guidelines for management of BAP1-TPDS [Lalloo et al 2023].

Author History

Mohamed Abdel-Rahman, MD, PhD (2016-present)
Lindsey Byrne, MS, CGC (2024-present)
Maria I Carlo, MD (2020-present)
Colleen Cebulla, MD, PhD (2016-present)
Helen Hanson, MD (2024-present)
Robert Pilarski, MS, LGC, MSW (2016-present)
Karan Rai, BS; The Ohio State University (2016-2020)

Revision History

• 5 December 2024 (sw) Comprehensive update posted live
• 17 September 2020 (sw) Comprehensive update posted live
• 13 October 2016 (bp) Review posted live
• 3 May 2016 (rp) Original submission

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