Non-syndromic Autosomal Recessive Intellectual Diasbility via the TRAPPC9 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 15207 | TRAPPC9 | 81479 | 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.
Clinical Features and Genetics
Clinical Features
Non-syndromic autosomal recessive intellectual disability (NS-ARID; OMIM:613192) is a clinically and genetically heterogeneous group of cognitive disorders. Mutations in the TRAPPC9 gene result in a clinically homogenous form of autosomal recessive intellectual disability. Unifying features of TRAPPC9-related NS-ARID cases are: infantile hypotonia, dysmorphic facial appearance, microcephaly, obesity, moderate to severe ID, and thin corpus callosum and reduced cortical white matter (as revealed by brain MRI) (Marangi et al. Eur J Hu Genet 21(2):229-232, 2013). Variable features included delayed speech or walking, stereotyped motions and febrile seizures.
Genetics
NS-ARID is caused by loss-of-function mutations in the TRAPPC9 gene. AR-NSID is inherited in an autosomal recessive manner. The same p.R475* mutation has been reported in three independent families of Middle Eastern descent, suggesting it may be a founder mutation (Marangi et al., 2013). TRAPPC9 encodes the TRAPPC9 protein that is highly expressed in post-mitotic neurons (Mochida et al. Am J Hu Genet 85(6):807-902, 2009). Studies in yeast show that TRAPPC9 interacts with the NFkB-inducing kinase and is believed to modulate NFkB signaling (Philippe et al. Am J Hu Genet 85(6):903-908, 2009). NFkB signaling has varied roles throughout biology, notably in maintaining synaptic plasticity and promoting neurogenesis.
Clinical Sensitivity - Sequencing with CNV PG-Select
Currently there is no estimate of the frequency of TRAPPC9 mutations in NS-ARID cases. Analytical sensitivity may be high, as reported mutations are expected to be detected by Sanger sequencing (Human Gene Mutation Database).
16% (1 of 6) of the reported TRAPPC9 causative variants are gross deletions (Human Gene Mutation Database).
Testing Strategy
This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.
This test provides full coverage of all coding exons of the TRAPPC9 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for TRAPPC9 testing include patients with symptoms of NS-ARID in which family history is consistent with autosomal recessive inheritance. Relatives of affected individuals can also be tested to determine carrier status. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TRAPPC9.
Candidates for TRAPPC9 testing include patients with symptoms of NS-ARID in which family history is consistent with autosomal recessive inheritance. Relatives of affected individuals can also be tested to determine carrier status. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TRAPPC9.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TRAPPC9 | 611966 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Mental Retardation, Autosomal Recessive 13 | AR | 613192 |
Citations
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
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ORDER OPTIONS
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2) Select Additional Test Options
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