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Spinal Muscular Atrophy

Item Value
Approval req'd? No
Available Stat? No
Utilization Guidelines Tests with long turn-around times (ie. Molecular based tests and Microarrays) should only be requested on an inpatient if the result is going to affect the inpatient management.

If the patient will likely be discharged before the result will be available, the test should be requested after discharge. (NOTE: UCSF Medical Center is not reimbursed for inpatient testing).

An exception to the above may be appropriate if there is a possibility the patient will not survive to be discharged and the information is important for diagnosis and/or family decisions/management (ie. recurrence risk).
Test code SMAPCR
Performed by Medical Genomics - Molecular Diagnostics
In House Availability Run 1x per week, Monday or Wednesday, day shift only.
Method Real time PCR with TaqMan probes
Collection Instructions Do not collect sample in heparin. Keep sample refrigerated for overnight or longer storage.

For UCSF Samples (from remote sites) Click here for sample collection instructions

For NON-UCSF Samples Click here for Requisition form & Account set-up instructions. Note we only do institutional billing.
Container type Lavender top
Amount to Collect 5 mL blood
Sample type EDTA whole blood
Amniotic fluid
Cultures amniocytes
Chorionic villi
Cultured chorionic villi
Preferred volume
Blood 5 ml
Amniotic fluid 20 ml
Cultures amniocytes 2 T25 flasks
Chorionic villi 20 mg
Cultured chorionic villi 2 T25 flasks
Min. Volume
Blood 2 ml
Amniotic fluid 10 ml
Cultures amniocytes 1 T25 flasks
Chorionic villi 10 mg
Cultured chorionic villi: T25 flasks
UCSF Rejection Criteria Heparinized samples. Low confluence cultures.
Insufficient amount of amniotic fluid or chorionic villi
Processing notes Refrigerate sample. DO NOT centrifuge or freeze.
Normal range
SMN1 2 copies or more
SMN2 0 to 5 copies
Synonyms SMN1 telomeric; SMN1-T; SMN2 centromeric; SMN2-C; Werdnig-Hoffmann disease; SMA type I; Congenital axonal neuropathy
Turn around times 7-10 days
Additional information An interpretation of this test by a laboratory physician will automatically be performed and billed for separately.

Spinal muscular atrophy (SMA) is a neuromuscular disorder and a frequently inherited cause of infant mortality. SMA is characterized by degeneration of lower motor neurons in the spinal cord and brain stem, leading to muscle wasting and paralysis. The disorder is classified into four subtypes (I-IV) based on the age of onset, which can range from infancy to adulthood. In its most severe form (Type I), SMA leads to death in infancy. In other non-fatal forms, affected individuals become disabled. Treatment in these cases is aimed at slow progression of the disease.

SMA is an autosomal recessive disorder with a carrier rate in the United States of about 1 in 50, leading to disease in approximately 1 in 10,000 live births. The survival motor neuron 1 (SMN1) gene, located on chromosome 5, is deleted in 95-98% of individuals affected with SMA. In 2-5% of affected individuals, SMA is caused by compound heterozygosity for an SMN1 deletion and an intragenic deleterious mutation. While most individuals carry one copy of SMN1 on each chromosome, 3.2% of the carrier population carries two SMN1 copies on one chromosome and none on the sister chromosome (2+0 genotype).

Another gene termed SMN2 is adjacent to SMN1 and differs from it by only 5 base pairs. Furthermore, individuals can carry multiple copy numbers of SMN2, ranging from 0 to 5 copies per chromosome. Although SMN1 is the predominant SMA-causing gene, the presence of multiple copy numbers of SMN2 can influence the severity of SMA. Thus, molecular assays aimed at detecting SMA should also be capable of identifying SMN2 copy numbers.

SMN1 generates a full-length mRNA transcript whereas SMN2 produces predominantly a truncated mRNA that lacks exon 7 and only a small amount of full-length SMN2 mRNA. This difference results from a C to T substitution that disrupts an SMN2 RNA splice site that is required to effectively splice exon 7. As a result, SMN2 cannot fully compensate for the loss of SMN1. However, when SMN2 copy number is increased, the small amount of full-length SMN2 mRNA can result in enough SMN2 mRNA to result in a milder SMA phenotype.

The C to T difference in exons 7 of SMN1 and SMN2 forms the basis of a PCR assay that discriminates between SMN1 and SMN2. When coupled with real time PCR and TaqMan probes, this PCR assay becomes quantitative and allows the quantitation of SMN1 and SMN2 copy numbers.

This test was developed and its performance characteristics determined by the Clinical Laboratories at the Medical Center at UC San Francisco. It has not been cleared or approved by the U.S. Food and Drug Administration.
CPT coding 81401
LDT or Mod FDA? Yes
Last Updated 1/22/2014 9:00:07 AM
Entry Number 1375
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