Pontocerebellar Hypoplasia via the TSEN2 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 | |
|---|---|---|---|---|---|
| 7375 | TSEN2 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
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
Pontocerebellar hypoplasias (PCH) are a group of clinically and genetically heterogeneous neurodegenerative disorders characterized by abnormal development of the pons, cerebellum and cerebral cortex; progressive microcephaly; psychomotor developmental delay; and swallowing difficulties (Barth. 1993. PubMed ID: 8147499; Namavar et al. 2011. PubMed ID: 21368912). Several subtypes have been described based on the clinical presentation, progression, and pathological and molecular defects. However, clinical overlapping features among various subtypes have been reported, and some genes have been implicated in more than one subtype, suggesting that PCH constitute a spectrum (Burglen et al. 2012. PubMed ID: 22452838; Samanta and Willis. 2016. PubMed ID: 27570394).
PCH2 is the most common form of the syndrome (Barth et al. 1995. PubMed ID: 7854532; Namavar et al. 2011. PubMed ID: 20952379; Namavar et al. 2011. PubMed ID: 21749694). It is distinguished by dystonia, chorea and cerebral visual defects (Barth et al. 1990. PubMed ID: 2370559). Additional features include seizures, ataxia, hypotonia, muscle weakness and wasting, and nystagmus. Symptoms are usually apparent at birth and death occurs in early infancy or childhood.
Genetics
All pontocerebellar hypoplasias are transmitted with an autosomal recessive mode of inheritance. Pathogenic variants in the TSEN2 gene account for less than 2% of patients with PCH2 (Namavar et al. 2011. PubMed ID: 20952379). Only four causative variants have been reported to date: two missense and two truncating variants (Budde et al. 2008. PubMed ID: 18711368; Bierhals et al. 2013. PubMed ID: 23562994).
No pathogenic large deletions or regulatory variants have been reported in the TSEN2 gene.
The TSEN2 gene encodes one of four subunits of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The other subunits are TSEN15, TSEN34, and TSEN54 (Paushkin et al. 2004. PubMed ID: 15109492).
Clinical Sensitivity - Sequencing with CNV PG-Select
Pathogenic variants in the TSEN2 gene account for less than 2% of patients with PCH2 (Namavar et al. 2011. PubMed ID: 20952379).
Thus far, no pathogenic gross deletions or duplications have been reported in the TSEN2 gene (Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the TSEN2 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 clinical features characteristic of PCH, a family history consistent with autosomal recessive mode of inheritance and no pathogenic variants in the TSEN54 gene; and family members of patients who have known TSEN2 pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TSEN2.
Candidates for this test are patients with clinical features characteristic of PCH, a family history consistent with autosomal recessive mode of inheritance and no pathogenic variants in the TSEN54 gene; and family members of patients who have known TSEN2 pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TSEN2.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TSEN2 | 608753 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Pontocerebellar Hypoplasia Type 2B | AR | 612389 |
Related Test
| Name |
|---|
| Pontocerebellar Hypoplasia Panel |
Citations
- Barth et al. 1990. PubMed ID: 2370559
- Barth et al. 1995. PubMed ID: 7854532
- Barth. 1993. PubMed ID: 8147499
- Bierhals et al. 2013. PubMed ID: 23562994
- Budde et al. 2008. PubMed ID: 18711368
- Burglen et al. 2012. PubMed ID: 22452838
- Human Gene Mutation Database (Bio-base).
- Namavar et al. 2011. PubMed ID: 21368912
- Namavar Y. et al. 2011. Brain: a Journal of Neurology. 134: 143-56. PubMed ID: 20952379
- Namavar Y. et al. 2011. Orphanet Journal of Rare Diseases. 6: 50. PubMed ID: 21749694
- Paushkin et al. 2004. PubMed ID: 15109492
- Samanta and Willis. 2016. PubMed ID: 27570394
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
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ORDER OPTIONS
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2) Select Additional Test Options
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