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Testing for Fragile X

During the 1970s and 1980s the only available tool for diagnosing Fragile X syndrome (FXS) was the chromosome (“cytogenetic”) test. While it was helpful, it was not always accurate. In the 1990s, scientists identified the FMR1 gene that causes FXS, and accurate DNA testing became available. The “FMR1 DNA Test” (sometimes called the “Fragile X DNA Test”) thus replaced chromosome testing, and became the “standard of care” for determining the presence of Fragile X. DNA testing detects more than 99 percent of individuals (both males and females) with FXS, as well as Fragile X carriers.

Who Should Have Fragile X Testing?

There are three general circumstances in which Fragile X testing should be considered:

  1. Clinical symptoms that suggest Fragile X Syndrome, FXTAS or infertility/FXPOI.
  2. A family history of Fragile X syndrome, FXTAS, intellectual or learning disabilities or autism of unknown cause, or infertility.
  3. Family or personal history of a Fragile X Genetics and Inheritance (carrier).

Specific indications for testing include:

  • Any male or female with intellectual disabilities, developmental delay, speech and language delay, autism or learning disabilities of unknown cause.
  • Any female with infertility, elevated FSH levels, premature ovarian failure, primary ovarian insufficiency or irregular menses.
  • Any adult over 50 with features of FXTAS, including intention tremors, ataxia, memory loss, cognitive decline, personality change, especially in combination with a positive family history of Fragile X.
  • Any preconception or pregnant woman who expresses interest in or requests Fragile X carrier testing.

Lab Tests for Fragile X

The FMR1 DNA Test can be administered with two different lab procedures.

  1. The Southern blot analysis test determines if the gene has a full mutation, its approximate size, whether the gene has been “methylated” and if there is mosaicism of the gene (a mixture of different cell types).
  2. The polymerase chain reaction (PCR) analysis can determine the actual number of “CGG repeats” (a pattern of DNA) that are present in the Fragile X gene. For various technical reasons, PCR has been not the test of choice to diagnose a full mutation, but is quite accurate in determining premutation and normal gene repeat numbers. However, PCR is less expensive and quicker than Southern blot, and recent advances in technology have increased its ability to identify Fragile X full mutations. PCR may thus be the only test used in the near future.

Testing Cost and Reporting Time

The blood test usually ranges from $300-$600, and results are usually available in 2-4 weeks.

How Are Testing Arrangements Made?

The test must be ordered by a genetic counselor or physician. A genetic counselor often will facilitate the testing, and make certain that the correct drawing, shipping and processing of the sample occurs. The genetic counselor is trained and experienced in the interpretation and explaining of the test results. She/he can coordinate any follow-up appointments and work with your physician to make referrals to resources in your area. You can locate a genetic counselor in your area by logging on to the “Find a counselor” feature on the National Society of Genetic Counselors website or by contacting the NFXF at or (800) 688-8765 for a referral to a counselor in your area.

In most cases you will be directed to go to a blood drawing station for a blood drawing procedure. Although this facility is often referred to as a “lab,” it is not the actual lab doing the DNA test. After the blood is drawn it is sent to a specific genetics or “reference” lab for the genetic test.

If your insurance company (or state/public insurance such as Medicaid) is paying for the testing, it is likely that the sample will go to the laboratory with which they are contracted. If you are paying for the test yourself, your physician or genetic counselor can locate a genetics lab in your area or one with which they have a relationship. The National Fragile X Foundation can assist your provider in locating a laboratory as well. For providers only, there is also a listing of laboratories that provide genetic testing; log onto GeneTests for information.

CPT and ICD-10 Codes for Fragile X Testing

When ordering the FMR1 DNA test, if the CPT codes are needed, check with the lab where the test will be performed. However, here is a list of the CPT codes most commonly associated with FMR1 DNA testing:

81243, 81244

Pertinent ICD-10 codes:

  • Fragile X Syndrome: Q99.2
  • Testing of male for genetic disease carrier status: Z31.440
  • Testing for genetic disease carrier status of female: Z31.430

What Do Test Results Report?

The test will determine the number of CGG repeats that are present in the area of the Fragile X gene that is studied. If Southern blot is ordered, the test will also tell you the methylation pattern of the Fragile X gene. If the testing is performed on a female, two numbers will be provided—one for each X chromosome. In males, only one result will be provided, though that number might be a range, such as 200-400, because the gene often expands in an unpredictable manner.


Who Receives Test Results?

Test results go to the provider who ordered the test, such as the genetic counselor or physician. Other recipients may include a pediatrician, obstetrician, or other health care provider involved in the patient’s or family’s care.

Other Tests for Children With Developmental Delay

Physicians and other providers ordering Fragile X testing often arrange for other genetic testing to provide more information on a child’s condition. Depending on the child’s presenting features or symptoms, this might include chromosome analysis, chromosome microarray (CGH), FISH testing (for other single gene conditions such as Velo-cardio-facial syndrome) and metabolic/ biochemical tests. Other types of medical evaluations might be recommended as well, including magnetic resonance imaging (MRI), electroencephalography (EEG), computer tomography (CT scan) or X-rays.

Chromosomal Microarray Analysis and the DNA Test for Fragile X

Chromosomal microarray analysis is a powerful test for detecting certain genetic causes of developmental disabilities; however, it is not able to detect Fragile X mutations of any kind.

For this reason, the diagnostic work-up of children with autism, global developmental delay, or intellectual disabilities should include both a microarray analysis and a separate Fragile X DNA analysis. If your child just had the microarray analysis but not the specific DNA test for Fragile X, then he has not been checked for Fragile X.