Invitae CHOPS Syndrome Test

Ordering
  • Test code: 04743
  • 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
Billing

Test description

The Invitae CHOPS Syndrome Test analyzes the AFF4 gene which is associated with cognitive impairment, coarse facies, heart defects, obesity, pulmonary involvement, short stature, and skeletal dysplasia (CHOPS).

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)

AFF4

Alternative tests to consider

Given the significant phenotypic overlap between Cornelia de Lange syndrome (CdLS) and CHOPS syndrome and the difficulty in differentiating between these syndromes early in life, analyzing the genes associated with Cornelia de Lange syndrome may be appropriate. These genes can be ordered with this test at no additional charge.

  • CHOPS syndrome

CHOPS syndrome is a congenital disorder with features including microcephaly, cognitive impairment, cataracts, hearing loss, obstructive sleep apnea, congenital heart defects, and genitourinary and skeletal anomalies. Most affected individuals have short stature, obesity, and distinctive coarse facial features.

AFF4 is the only gene known to be associated with CHOPS syndrome. However, due to the rarity of this condition, the percent of CHOPS syndrome attributed to pathogenic variants in AFF4 is currently unknown.

CHOPS syndrome is inherited in an autosomal dominant manner.

CHOPS syndrome is very rare and the penetrance is not clearly established.

The prevalence of CHOPS syndrome is not clearly established.

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, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
AFF4 NM_014423.3