Test Catalog

Test ID: BAP1    
BAP1 Immunostain, Technical Component Only

Useful For Suggests clinical disorders or settings where the test may be helpful

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For the initial technical component only immunohistochemical (IHC) stain performed, the appropriate bill-only test ID will be reflexed and charged (IHTOI). For each additional technical component only IHC stain performed, an additional bill-only test ID will be reflexed and charged (IHTOA).

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

BRCA1-asssociated protein 1 (BAP1) is a deubiquitinating enzyme that is a member of the polycomb group proteins of transcriptional repressors and exhibits tumor suppressive activity. BAP1 is located on chromosome 3p21 where loss of 1 copy of the gene and inactivating mutations are associated with the increased risk and development of various tumors such as malignant mesotheliomas, uveal melanomas, clear cell renal cell carcinoma, and esophageal squamous carcinomas. In some of these cases, loss of nuclear staining for BAP1 has been reported.

Interpretation Provides information to assist in interpretation of the test results

This test includes only technical performance of the stain (no pathologist interpretation is performed). Mayo Clinic cannot provide an interpretation of tech only stains outside the context of a pathology consultation. If an interpretation is needed, refer to PATHC / Pathology Consultation for a full diagnostic evaluation or second opinion of the case. All material associated with the case is required. Additional specific stains may be requested as part of the pathology consultation, and will be performed as necessary at the discretion of the Mayo pathologist.


The positive and negative controls are verified as showing appropriate immunoreactivity and documentation is retained at Mayo Clinic Rochester. If a control tissue is not included on the slide, a scanned image of the relevant quality control tissue is available upon request. Contact 855-516-8404.


Interpretation of this test should be performed in the context of the patient's clinical history and other diagnostic tests by a qualified pathologist.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Loss of BAP1 expression as determined by immunohistochemistry will not be able to differentiate between germline and somatic mutation.


Age of a cut paraffin section can affect immunoreactivity. Stability thresholds vary widely among published literature and are antigen-dependent. Best practice is for paraffin sections to be cut within 6 weeks.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Carbone M, Ferris LK, Baumann F, et al: BAP1 cancer syndrome: malignant mesothelioma, uveal and cutaneous melanoma, and MBAITS. J Transl Med 2012;10:179-185

2. Koopmans AE, Verdijk RM, Brouwer RWW, et al: Clinical significance of immunohistochemistry for detection of BAP1 mutations in uveal melanoma. Mod Path 2014;27:1321-1330

3. Joseph RW, Kapur P, Serie DJ, et al: Clear cell renal cell carcinoma subtypes identified by BAP1 and PBRM1 Expression. Jl of Urology 2015;195:1-8

4. Klebe S, Driml J, Nasu M, et al: BAP1 hereditary cancer predisposition syndrome: a case report and review of literature. Biomark Res 2015;3:14-20

5. Mori T, Sumii M, Fujishima F, et al: Somatic alteration and depleted nuclear expression of BAP1 in human esophageal squamous cell carcinoma. Cancer Sci 2015;106:1118-1129

6. Churg A, Sheffield BS, Galateau-Salle F: New markers for Separating Benign from Malignant Mesothelials: Are we there yet? Arch Pathol Lab Med 2016;140(4):318-321