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Rhabdoid Tumor Predisposition Syndrome via the SMARCB1 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SMARCB1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8357SMARCB181479 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.


Genetic Counselors


  • Yuan Xue, PhD

Clinical Features and Genetics

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).

Clinical Sensitivity - Sequencing with CNV PG-Select

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).

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).

Testing Strategy

This test provides full coverage of all coding exons of the SMARCB1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

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
Renal Cancer Panel
Schwannomatosis Panel


  • 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


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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