Rhabdoid Tumor Predisposition Syndrome via the SMARCB1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits


Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1202 SMARCB1$810.00 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
Germline mutations in the SMARCB1 gene have been found in 23-60% of individuals with rhabdoid tumors, with increased rates observed at an earlier ages of diagnosis (i.e. <6 months) (Bourdeaut et al. Clin Cancer Res 17:31-38, 2011). 

See More

See Less

Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 SMARCB1$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price













Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity
Clinical sensitivity for germline deletions and duplications of the SMARCB1 gene for familial and sporadic rhabdoid tumors is approximately 30% (11/35), with the majority of these being deletions (Eaton et al. Pediatr Blood Cancer 56(1): 7-15, 2011).

See More

See Less

Clinical Features
Rhabdoid tumors are rare aggressive tumors found in children. These tumors are histologically confirmed by having large cells with eccentrically located nuclei and abundant, eosinophilic cytoplasm (Beckwith et al. Cancer 41:1937–48, 1978); however the histology is heterogeneous and misclassification can occur . Originally rhabdoid tumors were found in the kidney and thought to be a variant of Wilms tumor (rhabdoid tumors of the kidney -RTK).  It is now known to be more aggressive kidney cancer. Whereas the overall survival rate for Wilms tumors exceeds 85%, the survival rate for renal malignant rhabdoid tumors is only 20-25%. Moreover, rhabdoid tumors have since been found in the liver, soft tissue, lung, skin, heart and the central nervous system (CNS). Approximately,10-15% of patients with malignant rhabdoid tumors have synchronous or metachronous brain tumors. In the CNS, where rhabdoid tumors are termed AT/RT (atypical teratoid, rhabdoid tumor), the most affected area is in the cerebellum.  Germline mutations in the SMARCB1 gene (also known as INI1 and hSNF5) are causative for Rhabdoid Tumor Predisposition Syndrome. Patients with germline SMARCB1 mutations have earlier-onset presentation versus sporadic rhabdoid tumors (6 months vs. 18 months) (Bourdeaut et al. Clin Cancer Res 17:31-38, 2011). SMARCB1 mutations may also predispose an individual for late-onset indolent schwannomas, a condition presenting with two or more benign tumors of the nerve sheath (Teplick et al. Eur J Pediatr 170:285–294, 2011).
Rhabdoid Tumor Predisposition Syndrome is an autosomal dominant disorder with incomplete penetrance caused by mutations in the SMARCB1 gene (Schneppenheim et al. Am J Hum Genet 86, 279–284, 2010) . Most mutations appear to be de novo, and gonadal mosaicism has been reported (Bourdeaut et al. Clin Cancer Res 17:31-38, 2011). SMARCB1 is a tumor suppressor that functions as a member of  the human ATP-dependent SWI/SNF complex, which has a role in epigenetic modification by regulating gene transcription and DNA repair (Reisman et al. Oncogene 28:1653–1668, 2009). Germline SMARCB1 mutations include missense, nonsense, splicing, regulatory, small and large deletions and duplications (Human Gene Mutation Database). Strong genotype-phenotypes do not exist, but splicing mutations and missense mutations have been found more predominantly in familial schwannomatosis, whereas truncating mutations are more frequently observed in individuals with rhabdoids (Bourdeaut et al. Clin Cancer Res 17:31-38, 2011).
Testing Strategy
The SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 is encoded by 9 exons (1-9) from SMARCB1 on chromosome 22q11.23.  Testing is accomplished by amplifying each coding exon and ~10 bp of adjacent noncoding sequence, then determining the nucleotide sequence using standard Sanger dideoxy sequencing methods and a capillary electrophoresis instrument. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Any individual who has been found to harbor rhabdoid tumors or an individual with a history of familial schwannomas. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.


Official Gene Symbol OMIM ID
SMARCB1 601607
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Familial Meningioma via the SMARCE1 Gene
Ovarian Cancer and Rhabdoid Tumor Predisposition Syndrome via the SMARCA4 Gene


Genetic Counselors
  • Beckwith JB, Palmer NF. 1978. Histopathology and prognosis of Wilms tumors: results from the First National Wilms’ Tumor Study. Cancer 41: 1937–1948. PubMed ID: 206343
  • Bourdeaut F, Lequin D, Brugières L, Reynaud S, Dufour C, Doz F, André N, Stephan J-L, Pérel Y, Oberlin O, Orbach D, Bergeron C, Rialland X, Fréneaux P, Ranchere D, Figarella-Branger D, Audry G, Puget S, Evans DG, Pinas JC, Capra V, Mosseri V, Coupier I, Gauthier-Villars M, Pierron G, Delattre O. 2011. Frequent hSNF5/INI1 germline mutations in patients with rhabdoid tumor. Clin. Cancer Res. 17: 31–38. PubMed ID: 21208904
  • Eaton KW, Tooke LS, Wainwright LM, Judkins AR, Biegel JA. 2011. Spectrum of SMARCB1/INI1 mutations in familial and sporadic rhabdoid tumors. Pediatr Blood Cancer 56: 7–15. PubMed ID: 21108436
  • Human Gene Mutation Database (Bio-base).
  • Reisman et al. (2009). "The SWI/SNF complex and cancer." Oncogene 28:1653–1668. PubMed ID: 19234488
  • Schneppenheim et al. (2010). "Germline nonsense mutation and somatic inactivation of SMARCA4/BRG1 in a family with rhabdoid tumor predisposition syndrome." Am J Hum Genet 86, 279–284. PubMed ID: 20137775
  • Teplick et al. (2011). "Educational paper: screening in cancer predisposition syndromes: guidelines for the general pediatrician." Eur J Pediatr 170:285–294. PubMed ID: 21210147
Order Kits

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  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 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 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 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

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 10 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.
  • 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.


(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.


(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.


(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.
loading Loading... ×