Androgen Insensitivity Syndrome (AIS) via the Androgen Receptor (AR) Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
736 AR$990.00 81405 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

This test is predicted to identify a pathogenic variant in 65% of all patients with Androgen Insensitivity Syndrome (Boehmer et al. 2001).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 AR$990.00 81479 Add to Order
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Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity

Although the clinical sensitivity of this array test is expected to be relatively low, at least eighteen gross deletions/duplications have been reported in the AR gene (Human Gene Mutation Database).

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Clinical Features

Male sexual differentation requires the Androgen Receptor (AR) and its ligands—Testosterone and Dihydroxytestosterone (DHT) (Wilson and Davies 2007). Testosterone, which is secreted by the developing testes beginning at 9 weeks of gestation, stimulates Wolffian duct differentiation into epididemis, vas deferens and seminal vesicles. DHT, derived from testosterone via the enzymatic activity of 5α-reductase type 2, stimulates prostate development and masculinization of the primordial external genital into penis and scrotum (Brinkmann et al. 2001). Both androgens exert their effect through binding and activation of the AR. In individuals with a 46,XY karyotype, defects in AR signaling result in Androgen Insensitivity Syndrome (AIS). AIS symptoms range from complete insensitivity (CAIS), whereby patients have female external genitalia, a short, blind ending vagina and no Wolffian duct derived structures, to partial insensitivity (PAIS), whereby patients can have a predominately female appearance with mild cliteromegaly, ambiguous genitalia, or an undervirilized male appearance (Galani et al. 2008). Given the complex nature of genital anomalies, recommendations for treatment and management of AIS should rely on an elaborate and individualized approach (Dacou-Voutetakis 2007). Genetic testing for the molecular cause of AIS is recognized as an invaluable aspect of this approach.


Pathogenic variants in the Androgen Receptor (AR) gene are the most common cause of Androgen Insensitivity Syndrome (AIS). To date, over 1,000 pathogenic variants have been described throughout the AR gene (Gottlieb et al. 2012). Nonsense and frameshift pathogenic variants cause complete AIS (CAIS), while weaker pathogenic variants, such as missense and regulatory (i.e. those in the promoter, introns, and 3’ untranslated region) variants, cause more variable symptoms and partial AIS (PAIS). Importantly, all documented AR pathogenic variants, and their respective phenotype, can be found in the Androgen Receptor Gene Mutations Database (ARDB,, making it possible for physicians and genetic counselors to offer a statistically relevant phenotype prognosis for most identified pathogenic variants. The AR gene is located on the X chromosome, so in most cases (~60%) the pattern of inheritance is X-linked recessive. However, an apparently high mutation rate within the AR gene also results in relatively frequent occurrence (~40%) of de novo pathogenic variants and somatic mosaicism (Audi et al. 2010). Identifying patients with de novo pathogenic variants and somatic mosaicism has important consequences for sex assignment and genetic counseling (Kohler et al.2005). Pathogenic variants in AR have been detected in 46,XY females. 46,XX carrier females are often unaffected.

Testing Strategy

This test involves bidirectional DNA sequencing of all 8 coding exons of the AR gene, plus ~10 bp of flanking non-coding DNA on either side of each exon. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.

Indications for Test

Candidates for this test are patients with a presumptive diagnosis of AIS (Boehmer et al. 2001).

This test is not designed to quantify the number of CAG or CCG trinucleotide repeats in exon 1, and is not appropriate for diagnosis of patients with Spinal and Bulbar Muscular Atrophy (SBMA).


Official Gene Symbol OMIM ID
AR 313700
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Androgen Resistance Syndrome XL 300068


Genetic Counselors
  • Audi L. et al. 2010. The Journal of Clinical Endocrinology and Metabolism. 95: 1876-88. PubMed ID: 20150575
  • Boehmer A.L. et al. 2001. The Journal of Clinical Endocrinology and Metabolism. 86: 4151-60. PubMed ID: 11549642
  • Brinkmann A.O. 2001. Molecular and Cellular Endocrinology. 179: 105-9. PubMed ID: 11420135
  • Dacou-Voutetakis C. 2007. Nature Clinical Practice. Endocrinology & Metabolism. 3: 668-9. PubMed ID: 17724484
  • Galani A. et al. 2008. Hormones (athens, Greece). 7: 217-29. PubMed ID: 18694860
  • Gottlieb B. et al. 2012. Human Mutation. 33: 887-94. PubMed ID: 22334387
  • Human Gene Mutation Database (Bio-base).
  • Köhler B. et al. 2005. The Journal of Clinical Endocrinology and Metabolism. 90: 106-11. PubMed ID: 15522944
  • Wilson C.A, Davies D.C. 2007. Reproduction. 133: 331-59. PubMed ID: 17307903
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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