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Spinal Muscular Atrophy (SMA) via MLPA of SMN1 and SMN2

Summary and Pricing

Test Method

Multiplex Ligation-Dependent Probe Amplification Assay
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SMN1 and SMN2 81329 81329 $540
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
6064SMN1 and SMN281329 81329 $540 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

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


  • Angela Gruber, PhD

Clinical Features and Genetics

Clinical Features

Spinal muscular atrophy (SMA) is a neuromuscular disorder characterized by muscle weakness (hypotonia, areflexia/hyporeflexia, tongue fasciculations, history of motor difficulties) that is symmetric, and progressive (Prior and Finanger. 2016. PubMed ID: 20301526). This weakness can affect the ability to crawl, walk, sit up, and control head movements, and additional clinical features include growth failure, restrictive lung disease, scoliosis, joint contractures, and sleep difficulties (Feng et al. 2017. PubMed ID: 28125085). Onset ranges from before birth to young adulthood, with later onset correlating to a less severe phenotype (Prior and Finanger. 2016. PubMed ID: 20301526). SMA affects approximately 1 in 6,000-10,000 births depending on ethnicity (Prior et al. 2011. PubMed ID: 21673580). There are five different classifications of SMA; however, a clear delineation into the subtypes is not always possible and the phenotypes represent more of a spectrum. SMA type 0 presents with severe weakness and hypotonia at birth, and early respiratory failure is common. There may be decreased fetal movement and joint contractures as well. SMA type 1 exhibits onset before 6 months of age. These individuals can only sit with support, and they can have normal or minimal facial weakness, difficulties sucking and swallowing, and mild joint contractures. SMA type 2 has an onset between 6-18 months. These individuals can sit independently after they are placed and can have postural finger tremors. SMA type 3 has onset after 18 months of age. These individuals can walk and move independently. SMA type 4 has onset in adulthood. Patients present with a milder form of muscle weakness (Prior and Finanger. 2016. PubMed ID: 20301526).


SMA is inherited in an autosomal recessive manner. However, approximately 2% of SMA patients have de novo pathogenic variants (Prior and Finanger. 2016. PubMed ID: 20301526). About 95-98% of individuals with SMA have a homozygous deletion of exon 7 of the SMN1 gene, which encodes the full length survival motor neuron protein (Prior and Finanger. 2016. PubMed ID: 20301526). The remaining 2% to 5% percent of individuals with SMA are compound heterozygotes for the SMN1 exon 7 deletion and an intragenic missense, nonsense or frameshift variant in SMN1 (Ogino and Wilson. 2004. PubMed ID: 14711346).

SMN1 is located in a complex region of chromosome 5 at band q13.2 that includes the homologous SMN2 gene. SMN1 and SMN2 are arranged in an inverted duplication, with SMN1 being telomeric to SMN2. These two genes differ by only 5 nucleotides, which includes a single variant (c.840C>T) in the coding sequence of SMN2 that affects splicing of SMN2. Consequently, SMN2 can only produce a fraction of the amount of full length transcripts compared to SMN1. In patients with a homozygous deletion of SMN1, the number of copies of SMN2 can modulate the clinical severity of the disorder. This observation has led to the development of new therapies for SMA designed to increase expression from SMN2. Consequently, assessment of the copy number of both SMN1 and SMN2 is clinically relevant in affected individuals (Talbot and Tizzano. 2017. PubMed ID: 28644430).

Clinical Sensitivity - MLPA

SMN1 deletions will be detected in over 99% of individuals with Spinal Muscular Atrophy in either the homozygous state (95% to 98% of affected individuals) or in the compound heterozygous state with another pathogenic variant (2% to 5% of affected individuals) (Rudnik-Schoneborn et al. 2012. PubMed ID: 22510849).

Testing Strategy

Multiplex Ligation-Dependent Probe Amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten 2011. PMID: 20938835). It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR, and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. For additional information please see www.mlpa.com. This test involves copy number analysis of both the SMN1 and SMN2 genes.

This test is validated for blood, saliva, cell culture, and the DNA Genotek OCD-100 kit.

Indications for Test

This test is for diagnostic purposes and is intended for individuals with clinical symptoms of SMA. Clinical indication needs to be provided on the Test Requisition Form. SMN2 copy number will be reported only for patients with zero copies of SMN1 detected, or for symptomatic individuals with one SMN1 copy.

This test is not intended for carrier screening in the general population and will not provide residual risk. We will perform testing in family members of a molecularly confirmed SMA proband; however, the proband needs to be provided as a positive control. At this time, we do not offer prenatal testing.


Official Gene Symbol OMIM ID
SMN1 600354
SMN2 601627
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835
  • Feng et al. 2017. PubMed ID: 28125085
  • Ogino and Wilson. 2004. PubMed ID: 14711346
  • Prior and Finanger. 2016. PubMed ID: 20301526
  • Prior et al. 2011. PubMed ID: 21673580
  • Rudnik-Schoneborn et al. 2012. PubMed ID: 22510849
  • Talbot and Tizzano. 2017. PubMed ID: 28644430


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

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