Joubert Syndrome via the TMEM138 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 9007 | TMEM138 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Joubert Syndrome (JS) (OMIM 213300) is marked by hypotonia, abnormal ocular movements, neonatal respiratory difficulties, mental retardation, hypoplasia of the cerebellar vermis, and malformation of the brainstem. The brain malformations lead to the "molar tooth sign" on cranial MRI, which is the hallmark clinical feature of JS. Other variable JS features include cystic kidneys, nephronophthisis, retinal dystrophy, ocular coloboma, occipital encephalocele, polydactyly, ataxia, and hepatic fibrosis. For more information, see Parisi and Glass (GeneReviews, 2013) and Parisi et al. (Eur J Hum Genet 15(5):511-521, 2007).
Genetics
JS is inherited in an autosomal recessive manner. Missense and splicing mutations in the TMEM138 gene cause JS (Lee et al. Science 355(6071):966-969, 2012). The TMEM138 gene encodes the transmembrane protein 138, which has been predicted to have a role in cilia-associated vesicle trafficking mechanisms. Fibroblasts with mutations in TMEM138 have short cilia and have a failure in ciliogenesis (Lee et al., 2012).
Clinical Sensitivity - Sequencing with CNV PGxome
Analytical sensitivity may be high because all TMEM138 mutations reported to date are expected to be detected by direct sequencing of genomic DNA. Clinical sensitivity is problematic to predict due to genetic heterogeneity and the paucity of documented cases (Lee et al. Science 355(6071):966-969, 2012).
No large deletion or duplication mutations have been reported to date in TMEM138 (Human Gene Mutation Database).
Testing Strategy
This test provides full coverage of all coding exons of the TMEM138 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 symptoms consistent with JS and family members of patients who have known mutations. Conclusive connections between clinical features and individual mutated genes have not yet been made. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TMEM138.
Candidates for this test are patients with symptoms consistent with JS and family members of patients who have known mutations. Conclusive connections between clinical features and individual mutated genes have not yet been made. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TMEM138.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TMEM138 | 614459 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Joubert syndrome 16 | AR | 614465 |
Citations
- Human Gene Mutation Database (Bio-base).
- Lee et al. (2012). "Evolutionarily assembled cis-regulatory module at a human ciliopathy locus." Science. 355(6071):966-969. PubMed ID: 22282472
- 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
- Parisi MA, Doherty D, Chance PF, Glass IA. 2007. Joubert syndrome (and related disorders) (OMIM 213300). Eur. J. Hum. Genet. 15: 511–521. PubMed ID: 17377524
Ordering/Specimens
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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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.