• Test code: 04749
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit

Invitae WAGR Syndrome Test

Test description

The Invitae WAGR syndrome test analyzes the WT1 and PAX6 genes, which are commonly deleted in a contiguous gene deletion within chromosomal region 11p13 and associated with Wilms tumor, aniridia, genitourinary anomalies and intellectual disability (WAGR) syndrome.

Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant can inform recurrence-risk assessment and genetic counseling.

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Primary panel (2 genes)
  • WT1-related disorders
    • WAGR syndrome (wilms tumor, aniridia, genitourinary, retardation)
    • isolated Wilms tumor
  • PAX6-related disorders
    • aniridia
    • Gillespie syndrome

WAGR syndrome is caused by a deletion on chromosome 11 inclusive of both WT1 and the PAX6 gene, which is associated with aniridia. Aniridia is characterized by bilateral underdevelopment or absence of iris tissue and is typically the first noticeable sign of WAGR syndrome. In individuals with WAGR syndrome, Wilms tumor presents earlier and is more often bilateral than in isolated Wilms tumor cases. Approximately 50-70% of these individuals develop Wilms tumor. Intellectual disability is common, as are psychiatric or behavioral problems. The most common genitourinary anomalies in males is cryptorchidism. Females may have underdeveloped ovarian tissue and bicornuate uterus, leading to fertility issues.

More than 50% of cases of WAGR syndrome are due to a contiguous gene deletion involving PAX6 and neighboring genes within chromosomal region 11p13, while approximately 14% of cases result from whole gene deletions of PAX6 and WT1.

WAGR syndrome is inherited in an autosomal dominant manner. Most occur as the result of a de novo pathogenic variant.

WAGR syndrome is completely penetrant.

WAGR syndrome occurs in 1 in 500,000 to 1 in one million individuals. Approximately one-third of those diagnosed with aniridia have underlying WAGR and roughly 1 in 143 cases of Wilms tumor are due to WAGR.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
PAX6 NM_000280.4
WT1 NM_024426.4