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XSense®, Fragile X with Reflex and Chromosome Analysis, Blood

Test code(s) 16326

This test is helpful as part of genetic evaluation for individuals with intellectual disability and/or autism with non-specific etiology. If individuals have a known family history of fragile X syndrome (FXS) or other FMR1-related disorders, it may be more appropriate to order “Fragile X With Reflex” without chromosome analysis. 

This test includes 2 components: fragile X FMR1 testing and chromosome analysis (karyotype).

A polymerase chain reaction (PCR)-based test is used to determine FMR1 CGG repeat number. If the CGG repeat size is under 85, the test will report out based on PCR data alone. If the CGG repeat size is 85 or greater, the test will reflex to methylation PCR to assess the methylation status of the FMR1 gene. Methylation PCR confirms whether an FMR1 expanded allele is hypermethylated, which would be expected in individuals with FXS. There is an additional charge (and CPT code) for the methylation PCR test.

Chromosome analysis (karyotype) is also performed, regardless of the fragile X results. 

The chromosome assay identifies

  1. Trisomies such as trisomy 21 (Down syndrome), trisomy 18, and trisomy 13
  2. Sex chromosome abnormalities such as Turner syndrome and Klinefelter syndrome
  3. Most rearrangements, including Robertsonian translocations, reciprocal translocations, and inversions
  4. Most marker chromosomes
  5. Mosaicism above 14% (95% confidence limit)1

The chromosome assay cannot detect

  1. Deletions/duplications smaller than the resolution of this assay
  2. Single-gene disorders such as cystic fibrosis, Marfan syndrome, neurofibromatosis, and others
  3. Small regions of homozygosity that are smaller than the threshold set by the laboratory (approximately 10 Mb)
  4. Mosaicism below 14% (95% confidence limit) 1

For more information, please call 1.866.GENE.INFO to speak with a genetic counselor.

FXS is the most commonly inherited cause of intellectual disability (including autism), affecting approximately 1:4,000 males and approximately 1:8,000 females. Over 99% of cases of FXS are caused by the expansion of a trinucleotide CGG repeat in the FMR1 gene and is inherited in an X-linked dominant pattern.2 Other FMR1-related disorders include fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X–associated primary ovarian insufficiency syndrome (FXPOI).

FMR1 CGG repeat size is classified as follows: normal (5-44 repeats), gray zone (45-54), premutation (55-200), or full mutation (>200). The distinction between these ranges is not absolute. Expansions to the full mutation size are associated with hypermethylation of the FMR1 gene and loss of FMR1 gene activity, which leads to FXS. If a full mutation is detected, individuals with 1 X chromosome would be expected to have FXS; individuals with 2 X chromosomes have a more variable presentation, ranging from normal to affected. Female premutation carriers are at an increased risk of POI. Each offspring is at an increased risk of inheriting an FMR1 allele that is in the full mutation range. Males with a premutation are at risk for developing symptoms associated with FXTAS (onset middle-age). See below for more information regarding gray zone and negative results.

Female gray zone (also known as intermediate) allele carriers have 1 FMR1 allele with a CGG repeat in the normal range and the other with a CGG repeat size between 45 and 54. The stability of alleles with 45 to 54 CGG repeats is variable and cannot be predicted in an individual; it may be stable from generation to generation in some families. There have been no reported cases of a gray zone allele expanding to a full mutation in 1 generation. There have been a few reports of a gray zone allele expanding to a full mutation within 2 generations, but the likelihood is low.3

Male gray zone allele carriers have 1 allele that has between 45 and 54 CGG repeats. The stability of this allele is unknown; gray zone alleles may be stable when passed to daughters or may expand to a premutation.

The vast majority of female patients with a negative result (ie, 2 normal-range CGG repeats in the FMR1 gene) are not affected by FXS and are not carriers. A male patient with 1 FMR1 allele in the normal size range would not be expected to have FXS. This is true even if the patient has an intellectual disability. There are rare cases of mosaicism or FXS caused by a mutation other than a CGG expansion. If other potential causes of the clinical presentation have been ruled out and the patient has classic FXS features or a family history of FXS, please call a genetic counselor at 1.866.GENE.INFO to discuss.

Yes, there are other studies that may be appropriate. There are many causes for developmental disorders, some of which are genetic. In the absence of clinical suspicion for a specific genetic disorder, a microarray analysis may be performed to detect subtle deletions and duplications (Chromosomal Microarray, Postnatal, ClariSure® Oligo-SNP; test code 16478). If clinical suspicion exists for a specific disorder, there may be other genetic tests available. This patient/family may benefit from further genetic counseling or genetic evaluation. You may call 866.GENE.INFO to discuss this case with a Quest genetic counselor. 

Genetic counseling is recommended to discuss the options available for further testing, if appropriate.

Individuals who test positive for any FMR1-related disorder or who are found to have a chromosomal variation may benefit from genetic counseling for further discussion of risks to themselves and future generations. Individuals who test negative but have a personal or family history of intellectual disabilities may pursue genetic evaluation to look for alternative diagnoses.  


  1. Hook EB. Exclusion of chromosomal mosaicism: tables of 90%,  95% and 99% confidence limits and comments on use. Am J Hum Genet. 1977;29(1):94-97.
  2. Hunter JE, Berry-Kravis E, Hipp H, et al. FMR1 disorders. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle; 1993-2021.
  3. Fernandez-Carvajal I, Lopez Posadas B, Pan R, et al. Expansion of an FMR1 grey-zone allele to a full mutation in two generations. J Mol Diagn, 2009;11(4):306-310. doi:10.2353/jmoldx.2009.080174


This FAQ is provided for informational purposes only and is not intended as medical advice. A clinician’s test selection and interpretation, diagnosis, and patient management decisions should be based on his/her education, clinical expertise, and assessment of the patient.

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