Treacher Collins Syndrome via the TCOF1 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 11737 | TCOF1 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Treacher Collins syndrome (TCS, also called mandibulofacial dysostosis or Franceschetti-Kelin syndrome) is a craniofacial malformation disorder characterized by downward slanting palpebral fissures, lower eyelid colobomas, microtia, and malar and mandibular hypoplasia. Other features include cleft palate, malformation of external ear canals, and bilateral conductive hearing loss (Dixon 1996; Chang et al. 2012). Clinical presentations of TCS are highly variable. TCS shares some facial dysmorphic features with other syndromes such as Pierre-Robin, Miller, Nager, and Goldenhar syndromes. It can be further divided into three subtypes: TCS type 1 is inherited in an autosomal dominant manner and is caused by mutations in TCOF1. TCS type 2 is inherited in both autosomal dominant and autosomal recessive manners and is caused by mutations in POLR1D. TCS type 3 is inherited in an autosomal recessive form and is caused by mutations in POLR1C (Dixon et al. 1996; Dauwerse et al. 2011; Katsanis and Jabs 2012, Schaefer et al. 2014).
Genetics
TCS Type 1 is inherited in an autosomal dominant manner and is caused by mutations in the TCOF1 gene. Treacle coded by TCOF1, a putative nucleolar phosphoprotein, is involved in synthesis of ribosomal RNA and plays a critical role in early embryonic development, particularly in craniofacial development (Dixon et al. 2000 ; Sakai D and Trainor PA. 2009). To date, more than 200 unique causative mutations have been identified in TCS patients. These mutations are: missense (4%), nonsense (23%), splicing (16%), small deletion/insertions (57%) and large deletion (5%). ~60% of affected individuals have a de novo TCOF1 mutation (Beygo et al. 2012; Bowman et al. 2012; Human Gene Mutation Database; Katsanis and Jabs 2012; Vincent et al. 2014). Penetrance of TCOF1 pathogenic variants associated with TCS is high, but some individuals with non-penetrance or incomplete penetrance have been reported (Katsanis and Jabs 2012).
Clinical Sensitivity - Sequencing with CNV PGxome
TCOF1 mutations were found in ~70% of clinical diagnosed TCS cases, and large deletions are ~5% of reported TCOF1 mutations (Bowman et al. 2012; Katsanis and Jabs 2012).
Testing Strategy
This test provides full coverage of all coding exons of the TCOF1 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 Treacher Collins Syndrome, and the family members of patients who have known TCOF1 mutations.
Candidates for this test are patients with symptoms consistent with Treacher Collins Syndrome, and the family members of patients who have known TCOF1 mutations.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TCOF1 | 606847 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Treacher Collins Syndrome | AD | 154500 |
Citations
- Beygo J, Buiting K, Seland S, Lüdecke H-J, Hehr U, Lich C, Prager B, Lohmann DR, Wieczorek D. 2011. First Report of a Single Exon Deletion in TCOF1 Causing Treacher Collins Syndrome. Molecular Syndromology 2: 53–59. PubMed ID: 22712005
- Bowman M, Oldridge M, Archer C, O’Rourke A, McParland J, Brekelmans R, Seller A, Lester T. 2012. Gross deletions in TCOF1 are a cause of Treacher–Collins–Franceschetti syndrome. European Journal of Human Genetics 20: 769–777. PubMed ID: 22317976
- Chang C, Steinbacher D. 2012. Treacher Collins Syndrome. Seminars in Plastic Surgery 26: 083–090. PubMed ID: 23633935
- Dauwerse JG, Dixon J, Seland S, Ruivenkamp CAL, Haeringen A van, Hoefsloot LH, Peters DJM, Boers AC, Daumer-Haas C, Maiwald R, Zweier C, Kerr B, Cobo AM, Toral JF, Hoogeboom AJ, Lohmann DR, Hehr U, Dixon MJ, Breuning MH, Wieczorek D. 2010. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nature Genetics 43: 20–22. PubMed ID: 21131976
- Dixon J, Brakebusch C, Fässler R, Dixon MJ. 2000. Increased levels of apoptosis in the prefusion neural folds underlie the craniofacial disorder, Treacher Collins syndrome. Hum. Mol. Genet. 9: 1473–1480. PubMed ID: 10888597
- Dixon MJ. 1996. Treacher Collins syndrome. Human molecular genetics 5: 1391–1393. PubMed ID: 8875242
- Human Gene Mutation Database (Bio-base).
- Katsanis SH, Jabs EW. 2012. Treacher Collins Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301704
- Sakai D, Trainor PA. 2009. Treacher Collins syndrome: Unmasking the role of Tcof1/treacle. The International Journal of Biochemistry & Cell Biology 41: 1229–1232. PubMed ID: 19027870
- Schaefer E, Collet C, Genevieve D, Vincent M, Lohmann DR, Sanchez E, Bolender C, Eliot M-M, Nürnberg G, Passos-Bueno M-R, Wieczorek D, Maldergem L van, Doray B. 2014. Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome. Genetics in Medicine. PubMed ID: 24603435
- Vincent M, Collet C, Verloes A, Lambert L, Herlin C, Blanchet C, Sanchez E, Drunat S, Vigneron J, Laplanche J-L, Puechberty J, Sarda P, et al. 2014. Large deletions encompassing the TCOF1 and CAMK2A genes are responsible for Treacher Collins syndrome with intellectual disability. European Journal of Human Genetics 22: 52–56. PubMed ID: 23695276
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
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
Loading...
×
ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.