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Spondylocostal Dysostosis via the DLL3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
DLL3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8599DLL381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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.


Genetic Counselors


  • Juan Dong, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Spondylocostal dysostosis (SCD) (OMIM 277300, 608681, 609813) is characterized by abnormal segmentation of the vertebral column. Patients have short trunks with multiple vertebral defects and rib anomalies (Turnpenny et al. J Med Genet 40:333-339, 2003). An autosomal dominant and three autosomal recessive forms (types 1-3) of SCD are known. The most common recessive type (type 1) is caused by variants in the delta-like 3 (DLL3) gene.


SCD, type 1 is an autosomal recessive disorder. Responsible variants were identified in the DLL3 gene on chromosome 19 (Bulman et al. Nature Genet 24:438-441, 2000). About 25 different causative DLL3 variants have been reported. Although some are missense, the great majority are nonsense, splicing, and particularly, frameshift. Variants are located throughout the length of the gene. No variants are predominant. The genes responsible for recessive SCD, type 2 (MESP2) and type 3 (LFNG) have been identified, but to date only one causative variant has been reported in each of these genes. Insufficient cases have yet been studied to make firm conclusions about phenotypic differences among the three types.

Clinical Sensitivity - Sequencing with CNV PGxome

Sparrow et al. (Am J Hum Genet 78:28-37, 2006) reported that 20-25% of SCD patients have variants in DLL3. DLL3 variants appear to be by far the most common known cause of SCD.

Testing Strategy

This test provides full coverage of all coding exons of the DLL3 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

All SCD patients are candidates for this test. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in DLL3.


Official Gene Symbol OMIM ID
DLL3 602768
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Spondylocostal Dysostosis 1 AR 277300

Related Test

Spondylocostal Dysostosis via the HES7 Gene


  • Bulman, M. P., et.al. (2000). "Mutations in the human delta homologue, DLL3, cause axial skeletal defects in spondylocostal dysostosis." Nat Genet 24(4): 438-41. PubMed ID: 10742114
  • Sparrow, D. B., et.al. (2006). "Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype." Am J Hum Genet 78(1): 28-37. PubMed ID: 16385447
  • Turnpenny PD, Whittock N, Duncan J, Dunwoodie S, Kusumi K, Ellard S. 2003. Novel mutations in DLL3, a somitogenesis gene encoding a ligand for the Notch signalling pathway, cause a consistent pattern of abnormal vertebral segmentation in spondylocostal dysostosis. J Med Genet 40: 333-339. PubMed ID: 12746394


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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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