CHOPS Syndrome via the AFF4 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 15141 | AFF4 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
Testing run on PG-Select capture probes does not include exome-wide CNV analysis. Reflex is available to PGxome or an exome-based panel, or you can use this gene list to create a custom panel (click here).
Click here for costs to reflex to whole PGxome.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
CHOPS syndrome is characterized by cognitive impairment, coarse facies, heart defects, obesity, pulmonary involvement, short stature, and skeletal dysplasia (Izumi et al. 2015). CHOPS syndrome clinically overlaps with Cornelia de Lange syndrome, which is known to be caused by pathogenic variants in the NIPBL, SMC3, RAD21, SMC1A, HDAC8 and KMT2A genes in the cohesin complex.
Genetics
AFF4-related CHOPS syndrome is inherited in an autosomal dominant manner. The AFF4 protein coded by the AFF4 gene is a key component of the super elongation complex that regulates transcriptional processes during embryogenesis (Izumi et al. 2015). Only 3 unique de novo missense AFF4 variants were reported in 3 unrelated probands affected with CHOPS syndrome by exome sequencing (Izumi et al. 2015).
Clinical Sensitivity - Sequencing with CNV PG-Select
The mutation detection rate by sequencing should be high, because all three reported pathogenic variants are missense (Izumi et al. 2015). However, due to limited publications, clinical sensitivity is currently unknown.
Testing Strategy
This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.
This test provides full coverage of all coding exons of the AFF4 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for this test are patients with symptoms consistent with CHOPS syndrome, and the family members of patients who have known AFF4 pathogenic variants. Patients with clinical presentations similar to Cornelia de Lange syndrome, who have no pathogenic variants in the known Cornelia de Lange syndrome related genes are also candidates.
Candidates for this test are patients with symptoms consistent with CHOPS syndrome, and the family members of patients who have known AFF4 pathogenic variants. Patients with clinical presentations similar to Cornelia de Lange syndrome, who have no pathogenic variants in the known Cornelia de Lange syndrome related genes are also candidates.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| AFF4 | 604417 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| CHOPS Syndrome | AD | 616368 |
Citations
- Izumi K. et al. 2015. Nature Genetics. 47: 338-44. PubMed ID: 25730767
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
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.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
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.
For Requisition Forms, visit our Forms page
Specimen Types
Specimen Requirements and Shipping Details
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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
STAT and Prenatal Test Options are not available with Patient Plus.
No Additional Test Options are available for this test.