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Craniosynostosis via the TCF12 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
TCF12 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11735TCF1281479 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


  • Stela Berisha, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Craniosynostosis is a primary abnormality of skull growth involving premature fusion of the cranial sutures causing skull deformity. Craniosynostosis type 3 is caused by pathogenic variants in the TCF12 gene, and explains 32% and 10% of patients affected with bilateral and unilateral Craniosynostosis, respectively (Sharma et al. 2013).


TCF12-related Craniosynostosis is inherited in an autosomal dominant manner. The TCF12 protein coded by the TCF12 gene is a member of the class A basic helix-loop-helix family, a partner of TWIST1 protein, which may be involved in the initiation of neuronal differentiation. Approximately 40 TCF12 pathogenic variants have been reported. They are: missense (7%), nonsense: (32%), splicing (17%), small deletion/insertions (41%), and one unbalanced translocation involving the TFC12 gene (Sharma et al. 2013; di Rocco et al. 2014; Le Tanno et al. 2014; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

TCF12 heterozygous pathogenic variants were identified in 36 out of 38 studied affected probands and 14 of the detected variants occurred de novo (Sharma et al. 2013). TCF12 pathogenic variants explain 32% and 10% of patients affected with bilateral and unilateral Craniosynostosis, respectively. TCF12 pathogenic variants were also seen in almost 53% of tested family members who did not have craniosynostosis or other relevant features indicating high non-penetrance (Sharma et al. 2013). An unbalanced translocation t(2;15)(q21;q21.3) including deletion of the entire gene has been reported to cause coronal craniosynostosis and intellectual disability (Le Tanno et al. 2014).

Testing Strategy

This test provides full coverage of all coding exons of the TCF12 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 Craniosynostosis, and the family members of patients who have known TCF12 pathogenic variants (Bravenboer et al. 2015).


Official Gene Symbol OMIM ID
TCF12 600480
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Craniosynostosis 3 AD 615314


  • Bravenboer N, Micha D, Triffit JT, Bullock AN, Ravazollo R, Bocciardi R, Rocco M di, Netelenbos JC, Ten Dijke P, Sánchez-Duffhues G, Kaplan FS, Shore EM, Pignolo RJ, Seemann P, Ventura F, Beaujat G, Eekhoff EM, Pals G. 2015. Clinical Utility Gene Card for: Fibrodysplasia ossificans progressiva. Eur J Hum Genet. PubMed ID: 25604857
  • di Rocco F, Baujat G, Arnaud E, Rénier D, Laplanche J-L, Daire VC, Collet C. 2014. Clinical spectrum and outcomes in families with coronal synostosis and TCF12 mutations. European Journal of Human Genetics 22: 1413–1416. PubMed ID: 24736737
  • Human Gene Mutation Database (Bio-base).
  • Le Tanno P, Poreau B, Devillard F, Vieville G, Amblard F, Jouk P-S, Satre V, Coutton C. 2014. Maternal complex chromosomal rearrangement leads to TCF12 microdeletion in a patient presenting with coronal craniosynostosis and intellectual disability. Am. J. Med. Genet. 164: 1530–1536. PubMed ID: 24648389
  • Sharma VP, Fenwick AL, Brockop MS, McGowan SJ, Goos JAC, Hoogeboom AJM, Brady AF, Jeelani NO, Lynch SA, Mulliken JB, Murray DJ, Phipps JM, Sweeney E, Tomkins SE, Wilson LC, Bennett S, Cornall RJ, Broxholme J, Kanapin A; 500 Whole-Genome Sequences (WGS500) Consortium, Johnson D, Wall SA, van der Spek PJ, Mathijssen IM, Maxson RE, Twigg SR, Wilkie AO. 2013. Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis. Nat Genet 45: 304-307. PubMed ID: 23354436


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

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2) Select Additional Test Options

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