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Pontocerebellar Hypoplasia via the TSEN15 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
TSEN15 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11777TSEN1581479 81479,81479 $990 Order Options and Pricing

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).

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


  • Renee Bend, PhD

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.


All pontocerebellar hypoplasias are transmitted with an autosomal recessive mode of inheritance. Pathogenic variants in the TSEN15 gene were recently identified via whole-exome sequencing. A total of three missense variants were found in three unrelated consanguineous families from Pakistan, Saudi Arabia and Syria. Evidence for pathogenicity include co-segregation of the homozygous variants with the affected status, heterozygosity in parents, reduction of protein level, and almost complete loss of in-vitro enzyme activity (Breuss et al. 2016. PubMed ID: 27392077).

No pathogenic large deletions or regulatory variants have been reported in the TSEN15 gene.

The TSEN15 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 TSEN2, TSEN34, and TSEN54 (Paushkin et al. 2004. PubMed ID: 15109492).

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in TSEN15 appear to be rare. Recently, three missense variants were found in three unrelated consanguineous families (Breuss et al. 2016. PubMed ID: 27392077).

Testing Strategy

This test provides full coverage of all coding exons of the TSEN15 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 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 TSEN15 pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TSEN15.


Official Gene Symbol OMIM ID
TSEN15 608756
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Pontocerebellar Hypoplasia Type 2F AR 617026


  • Barth et al. 1990. PubMed ID: 2370559
  • Barth et al. 1995. PubMed ID: 7854532
  • Barth. 1993. PubMed ID: 8147499
  • Breuss et al. 2016. PubMed ID: 27392077
  • Burglen et al. 2012. PubMed ID: 22452838
  • 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 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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