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Non-Syndromic Autosomal Recessive Intellectual Disability via the TUSC3 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1516 TUSC3$750.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
One study estimates that TUSC3 mutations occur in 1% of NS-ARID cases in their Iranian cohort (Garshasbi et al. Am J Med Genet 155A(8):1976-1980, 2011).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 TUSC3$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote
Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity
60% (3 of 5) of the reported TUSC3 variants are gross deletions that would be detectable via microarray (Human Gene Mutation Database).

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Clinical Features
Non-syndromic autosomal recessive intellectual disability (NS-ARID) encompasses a heterogeneous group of disorders of largely unknown genetic cause. Core features of NS-IDR seen in patients with mutations in the TUSC3 gene are moderate to severe intellectual disability and delayed speech (Garshasbi et al. Am J Med Genet 155A(8):1976-1980, 2011). Notably, patients do not display other neurological problems and no brain morphology abnormalities are revealed by MRI. Variable features of NS-ARID seen in some TUSC3 patients are short stature, short frenulum and borderline microcephaly. NS-ARID patients live relatively normal lifespans, but in most cases cannot live independently.
Genetics
NS-ARID can be caused by recessive mutations in the TUSC3 gene. Nonsense mutations and deletions in TUSC3 have been identified in three families with NS-ARID and segregate with the disease phenotype (Garshasbi et al., 2011).

TUSC3 encodes a protein believed to be an ortholog of the yeast oligosaccharyltransferase 3 (Ost3) protein. However, mutations in TUSC3 have not been observed to affect glycosylation patterns of proteins in cultured cells, suggesting that human TUSC3 may not be involved in glycosylation (Garshasbi et al. Am J Hu Genet. 82(5):1158-1164, 2008; Molinari et al. Am J Hu Genet 82(5):1150-1157, 2008). In addition, NS-ARID patients lack core features seen in other well-characterized congenital disorders of glycosylation (CDG). Recent studies in mice suggest that TUSC3 may be important for the transport of magnesium ions into neurons (Zhou et al. PNAS 106(37):15750-15755, 2009). Thus, it is currently unclear how mutations in TUSC3 contribute to NS-ARID phenotypes.
Testing Strategy
Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~20bp of adjacent noncoding sequences. This testing strategy will reveal coding sequence changes, splice site mutations and small insertions or deletions in the TUSC3 gene, but will not detect large deletions in the TUSC3 locus. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
Candidates for TUSC3 testing include patients with symptoms of NS-ARID and a family history of NS-ARID consistent with autosomal recessive inheritance. Relatives of affected individuals can also be tested to determine carrier status.

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 611093

Related Test

Name
Non-syndromic Autosomal Recessive Intellectual Diasbility via the TRAPPC9 Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Garshasbi, M. et al. (2008). "A Defect in the TUSC3 Gene Is Assocaited with Autosomal Recessive Mental Retardation." Am J Hum Genet 82(5):1158-1164. PubMed ID: 18452889
  • Garshasbi, M. et al. (2011). "A Novel Nonsense Mutation in TUSC3 is Responsible for Non-Syndromic Autosomal Recessive Mental Retardation in a Consanguineous Iranian Family." Am J Med Genet 155A(8):1976-1980. PubMed ID: 21739581
  • Human Gene Mutation Database (Bio-base).
  • Molinari, F.l. et al. (2008). "Oligosaccharyltransferase-Subunit Mutations in Nonsyndromic Mental Retardation." Am J Hu Genet 82(5):1150-1157. PubMed ID: 18455129
  • Zhou, H. and Clapham, D.E. (2009). "Mammalian MagT1 and TUSC3 are required for cellular magnesium uptake and vertebrate embyronic development." PNAS 106(37):15750-15755. PubMed ID: 19717468
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


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.
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.
SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.
DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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