Pontocerebellar Hypoplasia via the TSEN54 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
7373 TSEN54 81479 81479,81479 $640 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7373TSEN5481479 81479(x2) $640 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

18 days on average for standard orders or 13 days 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.

PCH4 is characterized by severe features including hypertonia, clonus and cerebellar hypoplasia. Severe apnea usually results in early death (Namavar et al. 2011. PubMed ID: 20952379).

PCH5 was reported in one single non-consanguineous family of European ancestry with three affected children. In this family, symptoms included fetal-seizures-like activity starting as early as the 18th week of gestation, generalized symmetrical hypertonia, clonus, and absence of primitive reflexes. Death occurred during the first week of life as the result of severe apnea (Patel et al. 2006. PubMed ID: 16470708).


All pontocerebellar hypoplasias are transmitted with an autosomal recessive mode of inheritance. Pathogenic variants in the TSEN54 gene account for over 90% of patients with PCH2 and PCH4 (Budde et al. 2008. PubMed ID: 18711368; Namavar et al. 2011. PubMed ID: 21749694; Battini et al. 2014. PubMed ID: 23307886). To date 20 pathogenic variants have been reported. They include missense, nonsense and splicing variants, as well as small frameshift deletions and inframe insertions. No pathogenic large deletions or regulatory variants have been reported in the TSEN54 gene.

A splice site variant (c.468+2T>C) together with the common causative missense variant (c.919G>T, Ala307Ser) were shown to be the cause of the disease in the single PCH5 family that was previously reported (Namavar et al. 2011. PubMed ID: 21368912). See also Namvar et al. 2016 (PMID: 20301773).

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

Clinical Sensitivity - Sequencing with CNV PG-Select

Pathogenic variants in the TSEN54 gene account for over 90% of patients with PCH2 and PCH4 (Budde et al. 2008. PubMed ID: 18711368; Namvar et al. 2016. PubMed ID: 20301773). PCH5 appears to be rare. Only one family with PCH5 and pathogenic variants in TSEN54 has been reported to date (Namavar et al. 2011. PubMed ID: 21368912).

Thus far, no pathogenic gross deletions or duplications have been reported in the TSEN54 gene (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the TSEN54 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 and a family history consistent with autosomal recessive mode of inheritance; and family members of patients who have known TSEN54 pathogenic variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TSEN54.


Official Gene Symbol OMIM ID
TSEN54 608755
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Pontocerebellar Hypoplasia Panel


  • Barth et al. 1990. PubMed ID: 2370559
  • Barth et al. 1995. PubMed ID: 7854532
  • Barth. 1993. PubMed ID: 8147499
  • Battini et al. 2014. PubMed ID: 23307886
  • 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
  • Namvar et al. 2016. PubMed ID: 20301773
  • Patel et al. 2006. PubMed ID: 16470708
  • 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

Specimen Types

Specimen Requirements and Shipping Details

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View Ordering Instructions

1) Select Test Method (Backbone)

1) Select Test Type

2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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