Table 1.

Summary of Molecular Genetic Testing Used in Spinal Muscular Atrophy

Gene 1Test MethodMutations Detected 2Mutation Detection Frequency by Test Method 3, 4
HomozygotesCompound Heterozygotes
SMN1Targeted mutation analysisDetects deletion of exon5~95%-98% ~2%-5%
Sequence analysisSequence variants 6, 7, 8.0%
Deletion/duplication analysis 9Copy numberNA(Note: for SMA carrier testing)
SMN2Deletion/duplication analysis 9Copy number 10NANA
1.

See Table A. Genes and Databases for chromosome locus and protein name.

2.

See Molecular Genetics for information on allelic variants.

3.

The ability of the test method used to detect a mutation that is present in the indicated gene

4.

Mailman et al [2002]

5.

Some laboratories list testing for deletion of both exon 7 and exon 8; however, it is NOT necessary to test for SMN1 exon 8 status (other than as a quality control step).

6.

Examples of variants detected by sequence analysis may include small intragenic deletions/insertions and missense, nonsense, and splice site mutations; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

7.

Detects the 2%-5% of individuals who are compound heterozygotes for an intragenic mutation and an SMN1 deletion of at least exon 7.

8.

Sequence analysis does not detect deletion or duplication of an exon(s) or an entire gene. If an intragenic mutation is detected, it is necessary to verify that the mutation has occurred in SMN1 and not SMN2. This requires additional testing by a method that facilitates SMN1-specific and SMN2-specific amplification and sequence analysis.

9.

Testing that identifies deletions/duplications not readily detectable by sequence analysis of the coding and flanking intronic regions of genomic DNA; included in the variety of methods that may be used are: quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA) that includes this gene/chromosome segment.

10.

The number of copies of SMN2 ranges from zero to five. Quantitative PCR, a type of deletion/duplication analysis, is often used for the accurate determination of SMN2 copy number [Anhuf et al 2003].

From: Spinal Muscular Atrophy

Cover of GeneReviews®
GeneReviews® [Internet].
Pagon RA, Adam MP, Ardinger HH, et al., editors.
Seattle (WA): University of Washington, Seattle; 1993-2015.
Copyright © 1993-2015, University of Washington, Seattle. All rights reserved.

For more information, see the GeneReviews Copyright Notice and Usage Disclaimer.

For questions regarding permissions: ude.wu@tssamda.

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.