Congenital hypotonia panel: DM1, SMA, PWS1

Test #:


Turnaround Time:

2-3 weeks

Specimen Requirements:

Specimens should be shipped at room temperature in a leak-proof, rigid container with overnight delivery. To discuss minimum acceptable specimens for neonatal patients or for sample types not listed, please contact Allele Diagnostics.

  • Peripheral blood: 2-3 mL EDTA whole blood (Neonates: 1 mL EDTA)
  • Cord blood: 2-3 mL EDTA whole blood
  • DNA2: 5 μg
CPT Codes:

81331 x1, 81400 x1, 81404 x1

Ordering Requirements:
Condition Description:

The Congenital hypotonia panel consists of tests for three genetic conditions most often associated with isolated congenital hypotonia in newborns: myotonic dystrophy (type 1), spinal muscular atrophy, and Prader-Willi syndrome.

Myotonic dystrophy, type I (DM1) is the most common type of muscular dystrophy in adults and affects the skeletal and smooth muscle. Severity and age of onset vary widely, and the disease is broadly classified into 3 types: mild, classic, and congenital. The congenital form typically presents with hypotonia, muscle weakness, or respiratory distress, and may progress to include intellectual disability and early death. DM1 is an autosomal dominant disorder, associated with an expansion of an unstable trinucleotide (CTG) repeat in the DMPK gene. The size of the repeat expansion correlates with the severity of the phenotype. The congenital form of DM1 is caused by a DMPK allele with >1000 CTG repeats.

Spinal muscular atrophy (SMA) is characterized by a loss of motor nerves in the spinal cord and brain stem, which leads to symmetrical, progressive muscle weakness and atrophy. Approximately 95%-98% of those affected will have loss of both copies of the SMN1 gene. Approximately 2%-5% of patients are compound heterozygotes for an SMN1 deletion and an SMN1 intragenic mutation. The presence of a functioning SMN2 gene results in a small amount of full-length functional transcripts. Establishing the copy number of SMN2 can help determine phenotype severity in SMA patients and eligibility for therapies. This assay tests for the common SMN1 and SMN2 deletions.

Prader-Willi syndrome (PWS) is characterized by neonatal onset of severe hypotonia, feeding difficulty and failure to thrive, which may be preceded by decreased fetal movement in utero. An insatiable appetite may develop in later infancy or early childhood and can lead to obesity if not controlled. Children with PWS can have short stature, hypogonadism, small hands and feet, and mild to moderate intellectual disability. Many individuals with PWS may have recognizable patterns of behavior marked by stubbornness, and temper tantrums. However, in the neonatal period, the disorder may manifest only as isolated hypotonia, usually accompanied by feeding problems, with no obvious dysmorphic features. PWS is caused by absence of the paternally derived 15q11.2-q13 region by one of several genetic mechanisms. Approximately 70% of individuals have a deletion in the paternal 15q11.2-q13 region. Approximately 25%-35% of individuals have maternal uniparental disomy, receiving two copies of the maternal chromosome 15 and no paternal chromosome 15. Approximately 2% of individuals have other imprinting center defects or rarely, a balanced chromosome rearrangement involving chromosome 15.

Clinical Utility:
  • This test is indicated for newborns with isolated, congenital hypotonia.
Genes (4):


Test Description:

This hypotonia panel includes multiple assays:

  • Testing for DM1 is performed via a polymerase chain reaction (PCR) bracketing the DMPK CTG trinucleotide repeat region. In positive samples, a reflex to Southern blot is required to accurately size the repeats. This may require a secondary sample, additional time, and an additional charge.
  • Testing for SMA is performed using Multiplex Ligation-Dependent Probe Amplification (MLPA) to determine the copy number of exon 7 within SMN1 and SMN2. This methodology also includes probes for the rare allele of two polymorphisms g.27134T>G and g.27706-27707delAT (reference sequence NM_000344.3), whose presence indicates silent carrier status.
  • Testing for PWS is performed via methylation-sensitive PCR using the 1st exon of the SNRPN gene.

DM1: This test examines the CTG trinucleotide repeat region exclusively. No other mechanism has been described for DM1, and the test is considered diagnostic.  Myotonia caused by DM2 will not be detected with this test.

SMA: The clinical sensitivity of SMA testing via MLPA is ~95-98%. MLPA cannot detect any changes that lie outside the target sequence of the probes and will not detect copy number neutral inversions or translocations. Diagnostic errors can occur due to rare sequence variations. Single base pair substitutions, small deletions/duplications, regulatory region mutations, and deep intronic mutations will not be detected. This test is unable to determine chromosomal phase of SMN1 or SMN2 copies. Even if the variants associated with SMN1 duplication are detected, the test cannot definitively differentiate individuals with one or more copies of SMN1 on each chromosome from individuals with two or more copies of SMN1 on one chromosome and zero on the other (silent carriers). Residual risk of carrier status with 2 copies of SMN1 detected and both the presence or absence of the polymorphism is based on a patient’s ethnic background. Ethnicity-specific residual risks can be found here:  

PWS: Methylation analysis detects ~99% of cases of PWS, but will not detect cases of balanced chromosome rearrangements within the 15q11.2-q13 region. If a result is positive, further testing is required to identify the underlying molecular mechanism. Rare diagnostic errors can occur due to primer or probe site mutations or rare polymorphisms.

  • Feng Y et al., The next generation of population-based spinal muscular atrophy carrier screening: comprehensive pan-ethnic SMN1 copy-number and sequence variant analysis by massively parallel sequencing. Genet Med 19(8):936-44 (2017). PubMed: 28125085
  • GeneReviews
  • OMIM
  1. This test is performed at a partner lab of Allele Diagnostics.
  2. Allele Diagnostics accepts DNA samples prepared by other CLIA-certified laboratories for DNA-based testing. To provide clinicians with optimal results, we recommend using the Qiagen Gentra Puregene extraction kit. If upon receipt the DNA is found to be suboptimal, our staff will contact the clinician to discuss testing options.