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Pontocerebellar Hypoplasia via the SEPSECS 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
SEPSECS 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7919SEPSECS81479 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).

PCH2D is also known as progressive cerebellocerebral atrophy (PCCA). Clinical features include developmental delay, sleep disturbance, irritability, slurred speech, spastic quadriplegia, seizures, choreiform movements, dysmetria, tonic upgaze, nystagmus, hypotonia and intellectual disability. Optic nerve atrophy and mild secondary mitochondrial myopathy have been reported in some cases (Ben-Zeev et al. 2003. PubMed ID: 12920088; Agamy et al. 2010. PubMed ID: 20920667; Iwama et al. 2016. PubMed ID: 26888482; Pavlidou et al. 2016. PubMed ID: 26805434).


All pontocerebellar hypoplasias are transmitted with an autosomal recessive mode of inheritance. PCH2D is caused by pathogenic variants in the SEPSECS gene (Anttonen et al. 2015. PubMed ID: 26115735). To date, about 10 pathogenic variants have been identified. Half of the variants are missense and the other half are of the truncating type, including one single exon deletion (Human Gene Mutation Database).

SEPSECS encodes the SepSecS protein that is involved in mammalian brain development and function (Agamy et al. 2010. PubMed ID: 20920667; Zhang and Zarbl. 2008. PubMed ID: 19122877).

Clinical Sensitivity - Sequencing with CNV PG-Select

Pathogenic variants in the SEPSECS gene appear to be rare. Such variants have been reported in a total of 13 unrelated patients.

Copy number variants also appear to be rare. Only one single exon deletion has been reported to date (Iwama et al. 2016. PubMed ID: 26888482; Human Gene Mutation Database).

Testing Strategy

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


Official Gene Symbol OMIM ID
SEPSECS 613009
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Pontocerebellar Hypoplasia Type 2D AR 613811

Related Tests

AMPD2-Related Disorders via the AMPD2 Gene
Pontocerebellar Hypoplasia Panel


  • Agamy et al. 2010. PubMed ID: 20920667
  • Anttonen et al. 2015. PubMed ID: 26115735
  • Barth. 1993. PubMed ID: 8147499
  • Ben-Zeev et al. 2003. PubMed ID: 12920088
  • Burglen et al. 2012. PubMed ID: 22452838
  • Human Gene Mutation Database (Bio-base).
  • Iwama et al. 2016. PubMed ID: 26888482
  • Namavar et al. 2011. PubMed ID: 21368912
  • Pavlidou et al. 2016. PubMed ID: 26805434
  • Samanta and Willis. 2016. PubMed ID: 27570394
  • Zhang and Zarbl. 2008. PubMed ID: 19122877


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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