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Pontocerebellar Hypoplasia via the VPS53 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
VPS53 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7937VPS5381479 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.


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).

PCH2E, also known as cerebello-cerebral atrophy type2, is distinguished by the degeneration of both the grey and white matter of the cerebellum. Clinical features include profound mental retardation, severe developmental delay, progressive spastic quadriplegia with painful joint contractures, clonus, epileptic seizures, mild hypotonia, sleep disorder, and marked irritability. Symptoms appear during early infancy (Ben-Zeev et al. 2003. PubMed ID: 12920088; Feinstein et al. 2014. PubMed ID: 24577744).


All pontocerebellar hypoplasias are transmitted with an autosomal recessive mode of inheritance. PCH2E is caused by pathogenic variants in the VPS53 gene. To date, only two pathogenic variants have been identified, via whole exome sequencing, in four non-consanguineous families of Jewish Moroccan ancestry. Compound heterozygosity was detected in all affected individuals. The pathogenic variants include one missense and one splice site variant and appear to be common in the Jewish Moroccan population with a carrier rate of ~ 1:37 (Feinstein et al. 2014. PubMed ID: 24577744).

No large pathogenic deletions or regulatory variants have been reported involving the VPS53 gene.

The VPS53 gene encodes one of the four subunits that constitute the Golgi-associated retrograde protein complex, which is involved in retrograde transport from early and late endosomes to the trans-Golgi network (Pérez-Victoria et al. 2008. PubMed ID: 18367545).

Clinical Sensitivity - Sequencing with CNV PG-Select

Pathogenic variants in the VPS53 gene appear to be rare. Such variants have been reported in four families of Jewish Moroccan ancestry. Available data suggest that this variant is common in this population with a carrier rate of ~ 1:37 (Feinstein et al. 2014. PubMed ID: 24577744). Thus far, no pathogenic gross deletions or duplications have been reported involving the VPS53 gene (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the VPS53 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 pontocerebellar hypoplasia and a family history consistent with autosomal recessive mode of inheritance. Family members of patients who have known VPS53 pathogenic variants are also candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in VPS53.


Official Gene Symbol OMIM ID
VPS53 615850
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Pontocerebellar Hypoplasia Type 2E AR 615851

Related Tests

AMPD2-Related Disorders via the AMPD2 Gene
Pontocerebellar Hypoplasia Panel


  • Barth. 1993. PubMed ID: 8147499
  • Ben-Zeev et al. 2003. PubMed ID: 12920088
  • Burglen et al. 2012. PubMed ID: 22452838
  • Feinstein et al. 2014. PubMed ID: 24577744
  • Human Gene Mutation Database (Bio-base).
  • Namavar et al. 2011. PubMed ID: 21368912
  • Pérez-Victoria et al. 2008. PubMed ID: 18367545
  • 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

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

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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