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Intellectual Disability via the TECR 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
8757 TECR 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8757TECR81479 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). Nonsyndromic ID is defined by the presence of intellectual disability as the sole clinical feature; however, often times the distinction between syndromic and nonsyndromic ID remains difficult due to the subtle signs of syndromic ID (Kaufman et al. 2010. PubMed ID: 21124998).

Deficiency of synaptic glycoprotein TECR impairs the synthesis of very long chain fatty acids, leading to a form of nonsyndromic ID, known as mental retardation 14 (MRT14). The clinical features of MRT14 may include (but may not limited to) developmental delay, speech and language delay, poor fine motor skills (intention tremor), minimal reading and writing skills, and narrow palate (Çalışkan et al. 2011. PubMed ID: 21212097).

Genetics

MRT14 is an autosomal recessive disorder, caused by pathogenic variants in human trans-2,3-enoyl-CoA reductase gene (TECR). TECR maps to chromosome 19p13.12 and consists of 13 coding exons that translate a 308 amino acid polypeptide of TECR, a membrane protein with 6 transmembrane-domains, 3 luminal loops, and cytosolic N and C termini. TECR reduces trans-2,3-enoyl-CoA to saturated acyl-CoA, the final step of very long chain fatty acid synthesis; however, the protein may have additional function in the nervous system. To date, only one pathogenic missense variant has been reported. Using biochemical assays, Abe et al. has demonstrated that this variant affects optimal enzymatic activity, protein stability and thus impairs the synthesis of very long chain fatty acids, in turn, altering the sphingolipid profile (Abe et al. 2013. PubMed ID: 24220030).

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). Analytical sensitivity should be high because all pathogenic variants reported within this gene to date are detectable by sequencing.

To date, no gross deletion/duplication involving TECR has been reported. We expect the clinical sensitivity of this test to be <0.1% of ID cases.

Testing Strategy

This test provides full coverage of all coding exons of the TECR 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 the patients with nonsyndromic intellectual disabilities who are negative for any kind of cytogenetic abnormalities, copy number variations, and Fragile-X syndrome, and also for the family members of the patients who have TECR 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 TECR.

Gene

Official Gene Symbol OMIM ID
TECR 610057
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Mental Retardation, Autosomal Recessive 14 AR 614020

Citations

  • Abe et al. 2013. PubMed ID: 24220030
  • Çalışkan et al. 2011. PubMed ID: 21212097
  • Kaufman et al. 2010. PubMed ID: 21124998
  • Vissers et al. 2016. PubMed ID: 26503795

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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