• Test code: 04744
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit

Invitae Glass Syndrome Test

Test description

The Invitae Glass Syndrome test analyzes the SATB2 gene. Glass syndrome is characterized by intellectual disability and dysmorphic facial features.

Genetic testing of this gene 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 (1 gene)
  • Glass syndrome

Glass syndrome is a developmental disorder that includes severe, but variable, intellectual disability and dysmorphic facial features, including midface hypoplasia, downslanting palpebral fissures, cleft palate, micrognathia, and associated crowded teeth. Patients may also present with seizures, growth retardation, arachnodactyly, joint laxity and happy demeanor. All reported individuals with Glass syndrome have been shown to carry de novo heterozygous SATB2 mutations or deletions of cytogenetic region 2q32-2q33, most of which include the SATB2 gene. The clinical presentation may vary in individuals with different deletions within this region. Cytogenetic studies including array CGH, as well as panels that include genes that cause overlapping phenotypes should also be considered in individuals with a suspected diagnosis of Glass syndrome.

SATB2 is the only gene known to be associated with Glass syndrome. However, due to the rarity of this condition, the percent of Glass syndrome attributed to pathogenic variants in SATB2 is currently unknown.

Glass syndrome is inherited in an autosomal dominant pattern, and all documented genetic variants have been de novo.

The penetrance of this disease is uncertain, but is thought to be very high.

The prevalence of this disease is unknown.

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, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

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
SATB2 NM_015265.3