Tumor Predisposition Syndrome, Uveal Melanoma and Mesothelioma via the BAP1 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
8155 BAP1 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8155BAP181479 81479(x2) $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Hannah Cox, PhD

Clinical Features and Genetics

Clinical Features

Germline BRCA1–associated protein 1 (BAP1) mutations have been reported to be a cause of several cancer types, including uveal melanoma (UM), and mesothelioma. UM is the most common primary intraocular tumor in adults (Goldstein et al. Nature Genetics 43(10):925-926, 2011). Mesothelioma is a rare form of cancer that develops in the mesothelium, the protective lining that covers many of the internal organs of the body. It is usually caused by exposure to asbestos. Only a small fraction of individuals exposed to asbestos have mesothelioma, suggesting that individuals with this type of cancer may have a genetic predisposition caused by BAP1 germline mutations (Testa et al. Nature Genetics 43(10):1022-5, 2011). Other less frequent cancer types which BAP1 germline mutations may have a role in include cutaneous melanoma, non-melanoma skin, ovarian, breast, renal, pancreatic, lung carcinoma and meningiomas (Goldstein et al. Nature Genetics 43(10):925-926, 2011; Abdel-Rahman et al. J Med Genet 48:856-859, 2011). Germline BAP1 mutations may also be associated with a more aggressive ocular melanoma phenotype and a recurrent phenotypic complex of cutaneous/ocular melanoma, atypical melanocytic proliferations and other internal neoplasms (i.e. COMMON syndrome) (Njauw et al. Plos One 7(4): e35295, 2012). The complete phenotypic spectrum of tumors in BAP1 mutation carriers remains to be accurately defined. BAP1 germline mutations have been suggested to result in a single disorder with different cancer spectrums and varying degrees of penetrance (Wiesner et al. J Clin Oncol 30(32):e337-40, 2012).

Genetics

BAP1 is a tumor suppressor gene that encodes a deubiquitinating enzyme containing numerous functional domains, including the ubiquitin C-terminal hydrolase (UCH) domain, a host cell factor-1 (HCF-1) binding domain and binding domains for BRCA1 and BARD1. BAP1 has been functionally implicated in numerous biologic processes, including chromatin dynamics, DNA damage response, and regulation of the cell cycle and cell growth (Goldstein et al. Nature Genetics 43(10):925-926, 2011). BAP1-related diseases are inherited in an autosomal dominant manner. Interestingly, monosomy of chromosome 3 is the most common somatic alteration in UM, reported in about 50% of primary tumors, and associated with aggressive tumors (Abdel-Rahman et al. J Med Genet 48:856-859, 2011). Approximately 50% of uveal melanomas harbor somatic BAP1 mutations (Harbour et al. Science 330:1410-13, 2010), and somatic mutations have also been found in mesotheliomas (Bott et al. Nat Genet 43:668-672, 2011). Germline BAP1 mutations include nonsense, splicing, and small insertions and deletions (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

The clinical sensitivity of BAP1 germline mutations in patients with BAP1-related tumors is currently unknown.

Testing Strategy

This test provides full coverage of all coding exons of the BAP1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Individuals who are suspected of having BAP1-related tumors, especially uveal melanoma, and mesothelioma. This test is also suggested for individuals who have a family history of BAP1-related tumors or a confirmed BAP1 germline mutation within the family. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Gene

Official Gene Symbol OMIM ID
BAP1 603089
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Malignant Mesothelioma AD 156240
Tumor Predisposition Syndrome AD 614327

Related Tests

Name
Melanoma Panel
Renal Cancer Panel

Citations

  • Abdel-Rahman et al. (2011). PubMed ID: 21941004
  • Bott et al. (2011). PubMed ID: 21642991
  • Goldstein et al. (2011). PubMed ID: 21956388
  • Harbour et al. (2010). PubMed ID: 21051595
  • Human Gene Mutation Database.
  • Njauw et al. (2012). PubMed ID: 22545102
  • Testa et al. (2011) PubMed ID: 21874000
  • Wiesner et al. (2012). PubMed ID: 23032617

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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