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Intellectual Disability via the TUSC3 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
8383 TUSC3 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8383TUSC381479 81479,81479 $890 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 backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

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

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

Intellectual Disability (ID) is a heterogeneous group of neurodevelopmental disorders, characterized by congenital limitation in intellectual functioning (intelligence quotient, IQ ≤70), and adaptive behavior. It is diagnosed in ~1–3% of the population before 18 years of age (American Association of Intellectual and Developmental Disabilities, AAIDD). Traditionally, ID can be both non-syndromic (NS-ID) and syndromic (S-ID). However, it is often difficult to rule out the presence of more subtle neurological anomalies and psychiatric disorders in NS-ID patients, and additionally, symptoms of some S-ID cases may be very subtle, blurring the distinction between S-ID and NS-ID (Kaufman et al. 2010. PubMed ID: 21124998).

Defects in a subunit of the oligosaccharyltransferase (OTase) complex lead to Mental Retardation 7 (MRT7) (Molinari et al. 2008. PubMed ID: 18455129). The clinical features of MRT7 are variable from nonsyndromic to syndromic and may include (but may not be limited to) moderate to severe ID, delayed psychomotor development, speech delay, short stature, dysmorphic features such as deep set eyes, long face, thin philtrum, pointed chin, hypertelorism, short frenulum and camptodactyly, syndactyly, and autism (Najmabadi et al. 2007. PubMed ID: 17120046; Molinari et al. 2008. PubMed ID: 18455129; Garshasbi et al. 2008. PubMed ID: 18452889; Garshasbi et al. 2011. PubMed ID: 21739581; Jones et al. 2013. PubMed ID: 23806237; Yavarna et al. 2015. PubMed ID: 26077850; Al-Amri et al. 2016. PubMed ID: 27148795).

Genetics

Pathogenic variants in human Tumor Suppressor Candidate 3 gene (TUSC3) lead to MRT7. TUSC3 maps to chromosome 8p22 and consists of 10 coding exons that translate into a 348 amino acid polypeptide. TUSC3 protein, believed to be an ortholog of the yeast oligosaccharyltransferase 3 (Ost3), is a subunit of the oligosaccharyltransferase (OTase) complex. However, in vitro studies on cultured cells have showed normal glycosylation patterns with defective TUSC3, suggesting that human TUSC3 may not be involved in glycosylation (Garshasbi et al. 2008. PubMed ID: 18452889; Molinari et al. 2008. PubMed ID: 18455129). Later in vivo studies in mice have suggested that TUSC3 may play an important role in magnesium transportation into neurons (Zhou and Clapham. 2009. PubMed ID: 19717468). To date, out of fourteen pathogenic variants reported in human TUSC3 gene (Human gene Mutation database), almost 60% are gross deletions involving TUSC3, and the rest are frameshift, missense, and nonsense variants. The disease transmission pattern is autosomal recessive.

Clinical Sensitivity - Sequencing with CNV PGxome

This test is predicted to detect pathogenic variants in <0.1% of individuals with intellectual disability (ID). In this context, it is important to note that although pathological variants over 800 genes have been identified in individuals with ID, a genetic diagnosis is still lacking in most cases due to extreme clinical and genetic heterogeneity of the condition (Vissers et al. 2016. PubMed ID: 26503795). Approximately 40% of reported TUSC3 pathogenic variants are directly detectable by sequencing, whereas the remainder are gross deletions.

To date, eight gross deletions involving TUSC3 have been reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the TUSC3 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 primarily implicated for patients with intellectual disabilities who are negative for any kind of cytogenetic abnormalities, copy number variations, Fragile-X syndrome and also for the family members of the patients who have TUSC3 pathogenic variants. Prenatal diagnosis is possible, if the genetic diagnosis has been firmly established in an affected family member. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TUSC3.

Gene

Official Gene Symbol OMIM ID
TUSC3 601385
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Mental Retardation, Autosomal Recessive 7 AR 611093

Citations

  • Al-Amri et al. 2016. PubMed ID: 27148795
  • Garshasbi et al. 2008. PubMed ID: 18452889
  • Garshasbi et al. 2011. PubMed ID: 21739581
  • Human Gene Mutation Database (Bio-base).
  • Jones et al. 2013. PubMed ID: 23806237
  • Kaufman et al. 2010. PubMed ID: 21124998
  • Molinari et al. 2008. PubMed ID: 18455129
  • Najmabadi et al. 2007. PubMed ID: 17120046
  • Vissers et al. 2016. PubMed ID: 26503795
  • Yavarna et al. 2015. PubMed ID: 26077850
  • Zhou and Clapham. 2009. PubMed ID: 19717468

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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