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SETPB1 Mutation Analysis Test

Last updated May 29, 2017

Approved by: Krish Tangella MD, MBA, FCAP

It is unknown exactly how a mutation in SETPB1 causes Schinzel-Giedion syndrome. However, the SETPB1 Mutation Analysis Test aids in the diagnosis of this debilitating disorder by detecting mutations in the SETPB1 gene.


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

  • KIAA0437 Mutation Analysis Test
  • SET-Binding Protein Mutation Analysis Test
  • SETBP_HUMAN Mutation Analysis Test

What is SETPB1 Mutation Analysis Test? (Background Information)

  • SETPB1 mutation refers to an alteration in the SETPB1 gene. It is associated with the Schinzel-Giedion syndrome birth defect
  • The SETPB1 gene gives instructions for the SETPB1 protein (or SET binding protein 1). The only known function of SETPB1 is that it attaches to a protein called SET. Both SETPB1 and SET are found in cells throughout the body
  • Alterations in the SETPB1 gene may result in a SETPB1 protein that is defective. This is associated with Schinzel-Giedion syndrome, a serious birth defect affecting the brain and skeletal system.
  • It is unknown exactly how a mutation in SETPB1 causes Schinzel-Giedion syndrome. However, the SETPB1 Mutation Analysis Test aids in the diagnosis of this debilitating disorder by detecting mutations in the SETPB1 gene

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

  • In situ hybridization techniques, such as fluorescence in situ hybridization (FISH)
  • Immunohistochemistry (IHC)
  • Next-generation sequencing (NGS)
  • Methylation profiling
  • 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 depending on the method being used, 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 SETPB1 Mutation Analysis Test?

Following are the clinical indications for performing the SETPB1 Mutation Analysis Test: 

  • A distinctive facial appearance including a prominent forehead; "flatness" of the middle part of the face (midface retraction); and a short upturned nose
  • Hydronephrosis
  • Severe developmental delay and intellectual disability
  • Skeletal (bone) malformations, such as short limbs; valgus or varus foot deformity (the foot is twisted outward or inward, respectively); skull abnormalities; or broad ribs
  • Genitourinary abnormalities, such as undescended testicle(s); abnormally small penis; hypospadias; small uterus; underdeveloped inner and outer labia (folds) of the vagina; or displaced anus
  • Heart defects, such as septal defects (affecting the dividing walls of the heart); valve abnormalities; hypoplastic ventricles (underdeveloped bottom chambers of the heart) or patent ductus arteriosus
  • Seizures
  • Visual or hearing impairment
  • Excessive hair growth (hypertrichosis)
  • Nail abnormalities

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

  • To assist (and in some cases, confirm) the initial diagnosis
  • To check for or ascertain a family history of the condition
  • To distinguish other conditions that have similar features (signs and symptoms)
  • To help determine treatment options

How is the Specimen Collected for SETPB1 Mutation Analysis Test?

The type and source and specimen sample requirements will depend on the preference of the individuals and the preference of the testing lab. Thus, it may vary from one individual to another and from one lab to another. Therefore, it is important to contact the testing lab for exact specimen requirements, before initiating the collecting and testing process.

Following is the specimen collection process for SETPB1 Mutation Analysis Test:

  • Sample on which the test is performed may include:
    • Peripheral blood in individuals showing signs and symptoms suspected of the condition
    • Bone marrow biopsy specimen
    • For mitochondrial DNA testing, usually a muscle biopsy or a liver biopsy is preferred
    • In case of expectant mothers, prenatal testing through amniotic fluid and chorionic villi sampling
    • Fetal cord blood
    • Fresh tissue from biopsy
    • Fresh tissue from autopsy sample
    • Fresh tissue from fetal demise
    • Buccal brushes: Using the kit that is provided by the testing laboratory, buccal brushes can be used to collect the specimen, by scraping the inner cheek lining (buccal mucosa)
    • Oral rinse specimens
    • Body fluids such as saliva, tears, and semen
    • Dried blood spots: This specimen type is usually requested in situations where the collection and/or shipping of whole blood is not practical
    • In some cases, hair samples (with attached roots), finger nails, and buccal swabs, may be acceptable
    • Formalin-fixed paraffin-embedded solid tumor tissue (FFPE tumor tissue), often referred to as paraffin block of the tumor
    • Products of conception sample from aborted pregnancy
  • Process of obtaining the sample: As outlined by the laboratory testing facility
  • Preparation required: As outlined by the laboratory testing facility

Important information:

Limitations of specimen while testing for the condition

  • For blood specimens: Individuals, who have received platelet transfusions, red blood transfusion, or white blood (leukocyte) transfusion, should wait at least 4 weeks before providing a blood specimen
  • The following specimens may not be acceptable in individuals who have received heterologous bone marrow transplant (in the past):
    • Peripheral blood samples
    • Oral rinse specimens
    • Bone marrow biopsy specimens
  • Testing should not be performed on a transplanted organ/specimen, since the genetic material belongs to the donor and not to the individual being tested
  • Formalin-fixed paraffin-embedded solid tumor tissue: In many cases, FFPE tissue blocks are usually not acceptable. Please contact the testing lab to ascertain, if it is an acceptable sample specimen
  • In some cases, a different source of specimen 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.

Turnaround time for test results

  • Depending on the location of testing, it may take from 2 to 8 weeks from the time of sample collection, to obtain the test results

Sample storage information

  • 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 tissue specimen over time

Cost of SETPB1 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, whether your healthcare provider/facility is in-network or out-of-network of your insurance company
  • 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, if required

What is the Significance of the SETPB1 Mutation Analysis Test Result?

  • The presence of a mutation in the SETPB1 gene indicates a positive result for the SETPB1 Mutation Analysis Test. This may point to a diagnosis of Schinzel-Giedion 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 SETPB1 mutation and Schinzel-Giedion syndrome are rare. However, their exact frequency is unknown
  • Many laboratories may not have the capability to perform this test. Only highly-specialized labs with advanced facilities and testing procedures may offer 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:

http://www.dovemed.com/common-procedures/procedures-laboratory/

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)

Schinzel Giedion syndrome | Genetic and Rare Diseases Information Center (GARD) – an NCATS Program. (n.d.). Retrieved from https://rarediseases.info.nih.gov/diseases/117/schinzel-giedion-syndrome

Schinzel-Giedion syndrome - Genetics Home Reference. (n.d.). Retrieved from https://ghr.nlm.nih.gov/condition/schinzel-giedion-syndrome#statistics

SETBP1 gene - Genetics Home Reference. (n.d.). Retrieved from https://ghr.nlm.nih.gov/gene/SETBP1#

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