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Schimke Immunoosseous Dysplasia via the SMARCAL1 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
SMARCAL1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11697SMARCAL181479 81479,81479 $990 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 platform).

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

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

For Sanger Sequencing click here.

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


  • Megan Piazza, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Schimke immunoosseous dysplasia (SIOD; OMIM#242900) is a multisystem disorder characterized by spondyloepiphyseal dysplasia (SED) resulting in disproportionate short stature, nephropathy, and immunodeficiency. Radiographic features of SED may include ovoid and mildly flattened vertebral bodies, shallow dysplastic acetabular fossae, and small deformed capital femoral epiphyses. Nearly all affected individuals have progressive steroid-resistant nephropathy, usually developing within five years of the diagnosis of growth failure and terminating with end-stage renal disease (ESRD). The majority of SIOD patients have T-cell deficiency that is associated with risk for opportunistic infection, a common cause of death. SIOD involves a spectrum that ranges from an infantile or severe early-onset form with death early in life to a juvenile or milder later-onset form with survival into adulthood if renal disease is appropriately treated (Baradaran-Heravi et al. GeneReviews 2011).


Schimke immunoosseous dysplasia (SIOD) is inherited in an autosomal recessive manner. SMARCAL1 is the only gene currently known to be associated with SIOD. SMARCAL1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1) encodes HARP, the SNF2-related protein, which participates in DNA-nucleosome restructuring (Boerkoel et al. Nat Genet 30:215-220, 2002). Variants in SMARCAL1 are predicted to cause loss of function in HARP, the deficiency of which leads to increased DNA damage and hypersensitivity to DNA-damaging agents (Bansbach et al. Genes Dev 23:2405–2414, 2009). The majority of reported variants are missense, splicing, and truncating variants. A gross deletion has been documented as well (Boerkoel et al, 2002). Multiple studies have shown that genotype does not predict disease severity or outcome (Bökenkamp et al. Pediatr Nephrol 20:1724–1728, 2005; Lücke et al. Am J Med Genet A 135:202–205, 2005; Dekel et al. Pediatr Res 63:398–403, 2008, Baradaran-Heravi et al. Hum Mol Genet 21: 2572-2587, 2012).

Clinical Sensitivity - Sequencing with CNV PGxome

This test is predicted to detect disease variants in 50-60% of individuals with clinical features of SIOD (Clewing et al. Hum Mutat 28:273–283, 2007).

Testing Strategy

This test provides full coverage of all coding exons of the SMARCAL1 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

Candidates for this test are patients with clinical features consistent with SIOD, and family members of patients who have known SMARCAL1 variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SMARCAL1.


Official Gene Symbol OMIM ID
SMARCAL1 606622
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Schimke Immunoosseous Dysplasia AR 242900


  • Bökenkamp et al. Pediatr Nephrol 20:1724–1728, 2005 PubMed ID: 16237566
  • Bansbach et al. Genes Dev 23:2405–2414, 2009 PubMed ID: 19793861
  • Baradaran-Heravi et al. GeneReviews 2011 PubMed ID: 21914180
  • Baradaran-Heravi et al. Hum Mol Genet 21: 2572-2587, 2012 PubMed ID: 22378147
  • Boerkoel et al. Nat Genet 30:215-220, 2002 PubMed ID: 11799392
  • Clewing et al. Hum Mutat 28:273–283, 2007 PubMed ID: 17089404
  • Dekel et al. Pediatr Res 63:398–403, 2008, PubMed ID: 18356746
  • Lücke et al. Am J Med Genet A 135:202–205, 2005 PubMed ID: 15880370


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

No Additional Test Options are available for this test.

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