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Spondylocostal Dysostosis via the TBX6 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
TBX6 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11733TBX681479 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.

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

Congenital vertebral malformation (CVM) is a birth defect of the vertebral column with an estimated prevalence 0.13-0.51 per 1000 live births (Giampietro et al. 2009. PubMed ID: 19154516). It can be further divided into several groups such as Klippel-Feil syndrome and Spondylocostal Dysostosis. Fetal ultrasound can detect vertebrae defects as early as 13 weeks' gestation (Turnpenny et al. 2017. PubMed ID: 20301771).

Spondylocostal Dysostosis (SCD) involves segmentation defect(s) of the vertebrae. Patients with SCD have short trunks with multiple vertebral defects and rib anomalies (Turnpenny et al. 2017. PubMed ID: 20301771). SCD is further divided into six sub-groups caused by pathogenic variants in the DLL3, MESP2, LFNG, HES7, TBX6, and RIPPLY2 genes, respectively.

Molecular genetic testing is advantageous to establish a proper diagnosis for individuals with CVM or SCD.


Pathogenic variants in the TBX6 gene have been reported in several patients with autosomal recessive and dominant SCD, with autosomal recessive predominating (Lefebvre et al. 2017. PubMed ID: 27861764; Turnpenny et al. 2017 PubMed ID: 20301771; Sparrow et al. 2013. PubMed ID: 23335591). The 16p11.2 deletion involving TBX6 has been repeatedly reported in patients with congenital scoliosis (Wu et al. 2015. PubMed ID: 25564734; Al-Kateb et al. 2014. PubMed ID: 24458548; Takeda et al. 2017. PubMed ID: 28054739). In one study, a proximal 16p11.2 deletion involving TBX6 in the compound heterozygous state along with a common risk haplotype was found in 11% of studied sporadic congenital scoliosis cases (Wu et al. 2015. PubMed ID: 25564734). In addition, in 2 of 20 trios studied the deletion occurred de novo. Pathogenic variants in the TBX6 gene contribute to ~10% of SCD cases (Turnpenny et al. 2017 PubMed ID: 20301771).

The TBX6 protein, coded by the TBX6 gene, is a regulator for Notch signal pathway and a member of the T-box DNA-binding domain family. TBX6 plays an essential role in embryonic neural plate and somite development (Chapman and Papaioannou. 1998. PubMed ID: 9490412; O'Roak et al. 2012. PubMed ID: 22495309). Mice with absence of TBX6 die around embryonic day 10.5, and mice with heterozygous TBX6 null alleles present vertebral defects with incomplete penetrance (Sparrow et al. 2013. PubMed ID: 23335591). To date, ~ 20 potential causative variants in TBX6 have been documented in Human Gene Mutation Database (HGMD). They include missense, nonsense, splicing, and small frameshift deletions/duplications. Of note, the 16p11.2 deletion or duplication involving TBX6 has also been reported to be associated with several other conditions such as autism spectrum disorders, and congenital anomalies of the kidney and urinary tract. The deletions/duplications were reported to be de novo in some of these cases (O'Roak et al. 2012. PubMed ID: 22495309; Verbitsky et al. 2019. PubMed ID: 30578417).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in the TBX6 gene contribute to ~10% of SCD cases (Turnpenny et al. 2017 PubMed ID: 20301771).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the TBX6 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

Candidates for this test are patients with symptoms consistent with Spondylocostal Dysostosis. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TBX6. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known pathogenic variants or to confirm research results.


Official Gene Symbol OMIM ID
TBX6 602427
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Spondylocostal Dysostosis 5 AR, AD 122600


  • Al-Kateb et al. 2014. PubMed ID: 24458548
  • Chapman and Papaioannou. 1998. PubMed ID: 9490412
  • Giampietro et al. 2009. PubMed ID: 19154516
  • Human Gene Mutation Database (Biobase).
  • Lefebvre et al. 2017. PubMed ID: 27861764
  • O'Roak et al. 2012. PubMed ID: 22495309
  • Sparrow et al. 2013. PubMed ID: 23335591
  • Takeda et al. 2017. PubMed ID: 28054739
  • Turnpenny et al, 2017 PubMed ID: 20301771
  • Verbitsky et al. 2019. PubMed ID: 30578417
  • Wu et al. 2015. PubMed ID: 25564734


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