Classic view of this page
BAP1 Germline
Clinical Genetic Test
Help
offered by
Genetic Diagnostic Laboratory
View lab's test page
LinkOut
GTR Test Accession: Help GTR000530437.2
CANCERINHERITED DISEASEINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2017-05-08
View version history
Last annual review date for the lab: 2023-06-21 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation; Predictive; ...
Conditions (4): Help
BAP1-related tumor predisposition syndrome; Melanoma, uveal, susceptibility to, 1; Melanoma, uveal, susceptibility to, 2; ...
Genes (1): Help
BAP1 (3p21.1)
Methods (3): Help
Molecular Genetics - Deletion/duplication analysis: Microarray; ...
Target population: Help
Germline BAP1 mutations are associated with a predisposition to uveal …
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
Genetic Diagnostic Laboratory
View lab's website
View lab's test page
Test short name: Help
BAP1
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • In-State Patients
  • Licensed Physician
  • Nurse Practitioner
  • Out-of-State Patients
  • Physician Assistant
  • Public Health Mandate
  • Registered Nurse
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
Submit test-specific paperwork with sample of blood. See specific sample requirements and shipping information found on our website.
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Test Order Code, Lab contact for this test, Test strategy
Conditions Help
Total conditions: 4
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 3
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Microarray
Other
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3500XL
Targeted variant analysis
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3500XL
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Predictive; Screening
Target population: Help
Germline BAP1 mutations are associated with a predisposition to uveal melanoma and malignant mesothelioma. Other cancer risks that may be associated with a BAP1 germline mutation include cutaneous melanoma, atypical melanocytic tumors, renal and lung cancers.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
Our variant classification system which is based on the American College of Medical Genetics and Genomics guidelines (Genet Med. 2015 May;17(5):405-24). This includes evaluating the variant using in gene-specific mutation databases, ExAC, dbSNP, and 1,000 genomes, and software (SIFT, PolyPhen).

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Yes. Free testing for VUS in family members is offered on a case by case basis; information will be collected by the lab to see which family members are available and if their results will help assess for the significance of the variant.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes. Ordering physician will be notified by mail or email with updated information for variant.
Recommended fields not provided:
Clinical validity, Clinical utility, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Platform:
Agilent SurePrint G3 Human CGH Microarray Kit, 2x400K
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Unknown, as reports are limited for genetic testing of identified cases of BAP1 tumor predisposition syndrome.
Assay limitations: Help
The current assay can not detect small levels of mosaicism, exonic deletions or duplciations, and deep intronic mutations that can lead to aberrant splicing.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations Help
SIFT, PolyPhen, etc

Laboratory's policy on reporting novel variations Help
Novel variations will be reported with added interpretation based on variant type and in the context of known mutations for the specific gene.
Recommended fields not provided:
Test Confirmation, Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, PT Provider, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.