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Joubert Syndrome via the CPLANE1 (C5orf42) 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
CPLANE1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11027CPLANE181479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Joubert Syndrome (JBTS; OMIM 614615) is an autosomal recessive condition marked by mid-hindbrain malformation, retinal dystrophy, cystic renal disease, hepatic fibrosis and polydactyly (Doherty, 2009). Mid-hindbrain malformation, which can be readily identified as a “Molar Tooth Sign” (MTS) using Magnetic Resonance Imaging (MRI), typically leads to hypotonia, ataxia, abnormal eye movements and intellectual disability; MTS is pathognomonic for JBTS.


JBTS is known to be caused by at least 18 different genes (see GeneReviews, www.ncbi.nlm.nih.gov/projects/GeneTests). Mutations in CPLANE1 (C5ORF42) were identified in a cohort of 7 unrelated French Canadian families with classic features of JBTS (Srour et al. 2012). Interestingly, this cohort included the original JBTS family, first described by Marie Joubert in 1969, for which the molecular cause had remained elusive until this report. Three different mutations (c.4006C>T [p.Arg1336Trp], c.7400+1G>A, and c.4690G>A [p.Ala1564Thr]) were found in multiple individuals indicating that CPLANE1 is associated with a complex founder effect in the French Canadian population (Srour et al. 2012). The c.4690G>A variant, which we define as c.7957+288G>A according to HGVS convention, is located in the intron between exons 40 and 41 of the longest RefSeq isoform (NM_023073.3). Upon further inspection, Srour et al. (2012) concluded that this variant is located within an alternatively spliced exon (40b) and predicted to result in a missense change (Ala to Thr). Four affected individuals carried this c.4690G>A variant, in addition to one of three other mutations (c.7400+1G>A, Arg2493* or Arg1336Trp). Therefore, the authors conclude that the c.4690G>A variant is probably pathogenic, although it is possibly benign and linked to an undetected pathogenic mutation. Future work is still need to assess the pathogenicity of this variant. The major CPLANE1 isoform (NM_023073.3) is predicted to have 51 exons, and the protein is thought to consist of 3,198 amino acids. Very little is known about the C5ORF5 protein, although given the role of other JBTS proteins it is likely a component of the primary cilium.

Clinical Sensitivity - Sequencing with CNV PGxome

For French Canadian patients, the clinical sensitivity is predicted to be ~50% (Srour et al. 2012). For all other JBTS patients, the sensitivity is likely <1%.

Testing Strategy

This test provides full coverage of all coding exons of the CPLANE1 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

This test is for patients diagnosed with Joubert Syndrome (JBTS), especially patients of French Canadian descent. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CPLANE1.


Official Gene Symbol OMIM ID
CPLANE1 614571
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Joubert Syndrome AR 614615


  • Doherty. 2009. PubMed ID: 19778711
  • Parisi M, Glass I. 2013. Joubert Syndrome and Related Disorders. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301500
  • Srour M, et al. Mutations in C5ORF42 Cause Joubert Syndrome in the French Canadian Population. Am J Hum Genet 90:693-700, 2012 PubMed ID: 22425360


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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View Ordering Instructions

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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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