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SF3B1 Mutation Analysis Test

Last updated May 29, 2017

The SF3B1 Mutation Analysis Test helps detect abnormalities in the SF3B1 protein. It helps diagnose blood cell disorders such as myelodysplastic syndrome.

What are other Names for this Test? (Equivalent Terms)

  • Hsh155 Mutation Analysis Test
  • PRPF10 Mutation Analysis Test
  • SF3b155 Mutation Analysis Test

What is SF3B1 Mutation Analysis Test? (Background Information)

  • SF3B1 mutation refers to an alteration in the SF3B1 gene. It is associated with myelodysplastic syndrome, a type of blood disorder
  • The SF3B1 gene gives instructions for the SF3B1 protein. SF3B1 stands for splicing factor 3b subunit 1. As the name implies, this protein forms a portion (subunit) of a larger protein called factor 3b, which is involved in a process called splicing
  • Splicing is the process of joining together fragments of genetic information. Splicing is carried out by proteins during alternative splicing, whereby intermediate compounds in the conversion of genetic information into proteins (called mRNAs) are cut apart, certain parts discarded, and the remains put back together
  • The portions of mRNA that are discarded are called introns; those that remain are called exons. The final product is a mature mRNA that is ready to be converted into a protein
  • The SF3B1 protein is important because of its role in allowing alternative splicing to take place. Alternative splicing is especially important in the development of cells such as blood cells
  • Alterations in the SF3B1 gene may result in an SF3B1 protein that is defective. A defective SF3B1 protein causes the factor 3b protein complex to behave abnormally, which prevents alternative splicing and causes blood cells to develop incorrectly
  • The SF3B1 Mutation Analysis Test helps detect abnormalities in the SF3B1 protein. It helps diagnose blood cell disorders such as myelodysplastic syndrome

The molecular testing, in general, can be performed using a variety of methods. Some of these methods include:

  • In situ hybridization technique, such as fluorescence in situ hybridization (FISH)
  • Immunohistochemistry (IHC)
  • Next-generation sequencing (NGS)
  • Polymerase chain reaction (PCR)
  • Comparative genomic hybridization (CGH)
  • Karyotyping including spectral karyotyping
  • mRNA analysis
  • Tissue microarrays (TMAs)
  • Southern blot test
  • Northern blot test
  • Western blot test
  • Eastern blot test

The methodology used for the test may vary from one laboratory to another. 

Note: Molecular testing has limitations due to the molecular method and genetic mutational abnormalities being tested. This can affect the results on a case-by-case basis. Consultation with your healthcare provider will help in determining the right test and right molecular method, based on individual circumstances.

What are the Clinical Indications for performing the SF3B1 Mutation Analysis Test?

Following are the clinical indications for performing the SF3B1 Mutation Analysis Test: 

  • Fatigue
  • Shortness of breath
  • Unusual paleness (pallor) due to anemia
  • Easy or unusual bruising or bleeding
  • Pinpoint-sized red spots just beneath the skin caused by bleeding (petechiae)
  • Frequent infections

In general, the molecular genetic testing is undertaken in the following situations: 

  • To assist (and in some cases, confirm) the initial diagnosis
  • To distinguish other tumors/conditions that have similar histological features, when examined by a pathologist under the microscope
  • To help in determining treatment options
  • To confirm recurrence of the tumor: Tumor recurrence can either be at the original tumor site, or at a distant location (away from the initial site)

How is the Specimen Collected for SF3B1 Mutation Analysis Test?

Following is the specimen collection process for SF3B1 Mutation Analysis Test:

The specimen sample requirements may vary from lab to lab. Hence, it is important to contact the testing lab for exact specimen requirements, before initiating the testing process.

  • Sample on which the test is performed may include:
    • Fresh tumor tissue during biopsy
    • Formalin-fixed paraffin-embedded solid tumor tissue (FFPE tumor tissue), often referred to as paraffin block of the tumor
    • Unstained tissue slides
  • Process of obtaining the sample: As outlined by the laboratory testing facility
  • Preparation required: As outlined by the laboratory testing facility


  • In some cases, a different source of specimen (such as peripheral blood, bone marrow biopsy specimen, or other body fluids) may be acceptable to the laboratory performing the test
  • Occasionally, additional samples may be required to either repeat the test or to perform follow-up testing
  • Depending on the location of testing, it may take up to 2 weeks’ turnaround time, to obtain the test results
  • Many hospitals preserve the paraffin blocks for at least 7 years. In general, older paraffin blocks (over 5 years) may affect the detection of specific mutations, due to degradation of the tumor specimen over time

Cost of SF3B1 Mutation Analysis Test:

  • The cost of the test procedure depends on a variety of factors, such as the type of your health insurance, annual deductibles, co-pay requirements, out-of-network and in-network of your healthcare providers and healthcare facilities
  • In many cases, an estimate may be provided before the test is conducted. The final amount may depend upon the findings during the test procedure and post-operative care that is necessary (if any)

What is the Significance of the SF3B1 Mutation Analysis Test Result?

  • The presence of a mutation in the SF3B1 gene indicates a positive result for the SF3B1 Mutation Analysis Test. This may point to a diagnosis of myelodysplastic syndrome

The laboratory test results are NOT to be interpreted as results of a "stand-alone" test. The test results have to be interpreted after correlating with suitable clinical findings and additional supplemental tests/information. Your healthcare providers will explain the meaning of your tests results, based on the overall clinical scenario.

Additional and Relevant Useful Information:

  • The SF3B1 gene resides on a position of the chromosome called 2q33.1 i.e., the long (q) arm of chromosome 2 in location 33.1
  • Many laboratories may not have the capability to perform this test. Only highly-specialized labs with advanced facilities and testing procedures may perform this test

Certain medications that you may be currently taking may influence the outcome of the test. Hence, it is important to inform your healthcare provider, the complete list of medications (including any herbal supplements) you are currently taking. This will help the healthcare provider interpret your test results more accurately and avoid unnecessary chances of a misdiagnosis.

What are some Useful Resources for Additional Information?

Please visit our Laboratory Procedures Center for more physician-approved health information:


References and Information Sources used for the Article:

https://ghr.nlm.nih.gov/primer/testing/genetictesting (accessed on 05/10/2017)

https://www.cdc.gov/mmwr/preview/mmwrhtml/rr5806a1.htm (accessed on 05/10/2017)

http://www.nature.com/gim/journal/v10/n5/full/gim200852a.html (accessed on 05/10/2017)

http://pediatrics.aappublications.org/content/106/6/1494 (accessed on 05/10/2017)

(2014, November 11). Retrieved from www.mayoclinic.org/diseases-conditions/myelodysplastic-syndromes/basics/symptoms/con-20027168

SF3B1 gene - Genetics Home Reference. (n.d.). Retrieved from https://ghr.nlm.nih.gov/gene/SF3B1#location

Helpful Peer-Reviewed Medical Articles:

Carrano, A. V., et al. Measurement and purification of human chromosomes by flow cytometry and sorting. Proceedings of the National Academy of Sciences 76, 1382–1384 (1979)

Drets, M. E., & Shaw, M. W. Specific banding patterns of human chromosomes. Proceedings of the National Academy of Sciences 68, 2073–2077 (1971)

Druker, B. J. Perspectives on the development of a molecularly targeted agent. Cancer Cell 1, 31–36 (2002)

Parra, I., & Windle, B. High resolution visual mapping of stretched DNA by fluorescent hybridization. Nature Genetics 5, 17–21 (1993) doi:10.1038/ng0993-17

Pinkel, D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 20, 207–211 (1998) doi:10.1038/2524

Speicher, M. R., et al. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nature Genetics 12, 368–375 (1996) doi:10.1038/ng0496-368

Malcovati, L., Papaemmanuil, E., Bowen, D. T., Boultwood, J., Della Porta, M. G., Pascutto, C., ... & Gallì, A. (2011). Clinical significance of SF3B1 mutations in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms. Blood, 118(24), 6239-6246.

Papaemmanuil, E., Cazzola, M., Boultwood, J., Malcovati, L., Vyas, P., Bowen, D., ... & Godfrey, A. L. (2011). Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. New England Journal of Medicine, 365(15), 1384-1395.

Brecqueville, M., Rey, J., Bertucci, F., Coppin, E., Finetti, P., Carbuccia, N., ... & Verrot, D. (2012). Mutation analysis of ASXL1, CBL, DNMT3A, IDH1, IDH2, JAK2, MPL, NF1, SF3B1, SUZ12, and TET2 in myeloproliferative neoplasms. Genes, Chromosomes and Cancer, 51(8), 743-755.

Quesada, V., Conde, L., Villamor, N., Ordóñez, G. R., Jares, P., Bassaganyas, L., ... & López-Guerra, M. (2012). Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nature genetics, 44(1), 47-52.

Oscier, D. G., Rose-Zerilli, M. J., Winkelmann, N., de Castro, D. G., Gomez, B., Forster, J., ... & Else, M. (2013). The clinical significance of NOTCH1 and SF3B1 mutations in the UK LRF CLL4 trial. Blood, 121(3), 468-475.

Jeromin, S., Weissmann, S., Haferlach, C., Dicker, F., Bayer, K., Grossmann, V., ... & Kern, W. (2014). SF3B1 mutations correlated to cytogenetics and mutations in NOTCH1, FBXW7, MYD88, XPO1 and TP53 in 1160 untreated CLL patients. Leukemia, 28(1), 108-117.

Reviewed and Approved by a member of the DoveMed Editorial Board
First uploaded: May 29, 2017
Last updated: May 29, 2017