Ordering Recommendation

Prenatal diagnostic testing for spinal muscular atrophy (SMA) when both parents carry a deletion of SMN1 or have a previous child with SMA caused by a deletion of SMN1.

New York DOH Approval Status

This test is New York state approved.

Specimen Required

Patient Preparation

Fetal Cultured amniocytes or Cultured CVS AND Maternal Whole Blood Specimen: Lavender (EDTA), pink (K2EDTA), or yellow (ACD solution A or B).

Specimen Preparation

Cultured Amniocytes or Cultured CVS: Transfer cultured amniocytes or cultured CVS to two T-25 flasks at 80 percent confluence (Min: one T-25 flask at 80 percent confluence). Backup cultures must be retained at the client's institution until testing is complete. If ARUP receives a sample below the minimum confluence, Cytogenetics Grow and Send (ARUP test code 0040182) will be added on by ARUP, and additional charges will apply. If clients are unable to culture specimens, Cytogenetics Grow and Send should be added to initial order.
Maternal Whole Blood Specimen: Transport 2 mL whole blood. (Min: 1 mL)

Storage/Transport Temperature

Cultured Amniocytes or Cultured CVS: CRITICAL ROOM TEMPERATURE. Must be received within 48 hours of collection due to viability of cells.
Maternal Whole Blood Specimen : Room temperature.

Unacceptable Conditions

Cultured Amniocytes or Cultured CVS: Room temperature: 48 hours; Refrigerated: Unacceptable; Frozen: Unacceptable
Maternal Whole Blood Specimen: Room Temperature: 7 days; Refrigerated: 1 month; Frozen: Unacceptable


Multiplex Ligation-Dependent Probe Amplification (MLPA)




9-10 days
If culture is required, an additional 1 to 2 weeks is required for processing time.

Reference Interval

By report

Interpretive Data

Background information for Spinal Muscular Atrophy (SMA) Copy Number Analysis, Fetal
: Spinal muscular atrophy (SMA) is the most common lethal genetic disease in children. It is characterized by progressive muscle atrophy and weakness, poor weight gain, restrictive lung disease, scoliosis, and joint contractures due to degeneration of lower motor neurons and brain stem nuclei. Onset ranges from before birth to young adulthood and severity is highly variable. Individuals with SMA have no functional copies of the SMN1 gene either due to homozygous loss of SMN1 from deletion or gene conversion (95 percent) or loss of one SMN1 gene and a pathogenic sequence variant in the other (5 percent). The SMN2 gene produces a small amount of functional survival motor neuron protein compared to SMN1. An increased number of SMN2 gene copies may reduce disease severity but phenotype cannot be predicted with certainty.
Inheritance: Autosomal recessive.
Cause: Pathogenic variants in the SMN1 gene.
Variants Tested: For copy number: SMN1 (NM_000344.3) exon 7 c.840C and exon 8 c.*239G, and SMN2 (NM_017411.3) exon 7 c.840T.
Clinical sensitivity: 95-98 percent.
Methodology: Multiplex probe ligation-dependent amplification (MLPA).
Analytical sensitivity and specificity: 99 percent.
Limitations: Diagnostic errors can occur due to rare sequence variations. Single base pair substitutions, small deletions/duplications, regulatory region and deep intronic variants will not be detected. This test is unable to determine chromosomal phase of SMN1 or SMN2 copies.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Compliance Category

Laboratory Developed Test (LDT)


Hotline History


CPT Codes

81329; 81265 Fetal Cell Contamination (FCC)


Component Test Code* Component Chart Name LOINC
0050548 Maternal Contamination Study Fetal Spec 59266-7
0050612 Maternal Contam Study, Maternal Spec 66746-9
2013438 SMA Copy Number, Symptoms 75325-1
2013439 SMA Copy Number, SMN1 Copies 35462-1
2013440 SMA Copy Number, SMN2 Copies 54449-4
2013445 SMA Copy Number, Specimen 66746-9
2013446 SMA Copy Number, Interp 35462-1
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


Spinal Muscular Atrophy (SMA) Copy Number Analysis, Fetal