Ordering Recommendation

Use to determine X-chromosome inactivation (XCI) pattern for female carriers of X-linked disorders and assess pathogenicity of genetic variant in an X-linked gene. Test does not detect clonality.




Restriction Enzyme Digestion/Polymerase Chain Reaction/Fragment Analysis




10-14 days

New York DOH Approval Status

Specimens from New York clients will be sent out to a New York DOH approved laboratory, if possible.

Specimen Required

Patient Preparation

Lavender (EDTA), pink (K2EDTA), or yellow (ACD Solution A or B).

Specimen Preparation

Transport 3 mL whole blood. (Min: 1 mL)

Storage/Transport Temperature


Unacceptable Conditions

Ambient: 1 week; Refrigerated: 1 week; Frozen: Unacceptable

Reference Interval

By report

Interpretive Data

Interpretive Data:
Characteristics: Females usually have two copies of the X-chromosome, one of which becomes randomly inactivated early in embryonic development in a process known as lyonization. If either the paternally or maternally derived X-chromosome is preferentially inactivated, this results in a nonrandom or "skewed" pattern of X-chromosome inactivation (XCI). The pattern of XCI may vary among tissue types. XCI ratios of 50:50 to 74:26 suggest random XCI, ratios greater than 85:15 suggest nonrandom XCI, and ratios from 75:25 to 85:15 should be interpreted with caution.
Cause: Nonrandom XCI may result by chance or from secondary cell selection in females who are heterozygous for X-chromosome rearrangements, carriers of pathogenic variants in X-linked genes, or affected with neoplastic disease.
Gene Tested: The androgen receptor (AR) gene on the X chromosome.
Clinical Sensitivity: Approximately 90 percent. An estimated 10-15 percent of females have skewed X-inactivation by chance. However, skewed XCI may be seen more frequently with increasing age.
Methodology: Methylation-sensitive restriction digest followed by PCR and fragment analysis.
Limitations: Testing is limited to XX females only. This assay will be uninformative in up to 20 percent of females due to homozygosity for the polymorphic AR gene locus analyzed. XCI patterns may differ among tissues; therefore, the XCI ratio reported is for the tissue type tested with a standard deviation 0.08 for XCI ratios of 50:50-79:50; 0.05 for XCI ratios 80:20 or greater. Although this test will detect the methylation status of the X-chromosomes, it will not determine if the X-inactivation pattern is associated with rearrangements of the X chromosome, pathogenic variants in X-linked genes or neoplastic disease. If a nonrandom XCI pattern is present, the parent of origin of the active X cannot be determined without testing parental samples. XCI ratios should not be used to predict prognosis for female carriers of X-linked disorders as variable expressivity may result due to other genetic or environmental modifiers. Because the level of XCI may differ in prenatal specimens and whole blood, this test is not recommended for prenatal diagnosis. Diagnostic errors can occur due to rare sequence variations.

This test was developed and its performance characteristics determined by ARUP Laboratories. It has not been cleared or approved by the US Food and Drug Administration. This test was performed in a CLIA certified laboratory and is intended for clinical purposes.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Compliance Category

Laboratory Developed Test (LDT)


Hotline History


CPT Codes



Component Test Code* Component Chart Name LOINC
2006353 X-Chromosome Inactivation Specimen 66746-9
2006354 X-Chromosome Inactivation Interpretation 35455-5
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


X-Chromosome Inactivation Analysis