Spinal Muscular Atrophy (SMA) is a hereditary neuromuscular disorder characterized by the progressive loss of motor neurons, leading to muscle weakness and atrophy. SMA is caused by insufficient levels of the Survival Motor Neuron (SMN) protein, necessary for nerve cell function. This deficiency results from a problem with the SMN1 gene, the primary producer of this protein. All humans possess a nearly identical backup gene, SMN2. The number of functional copies of SMN2 serves as the most important genetic modifier of the SMA phenotype.
The Critical Difference Between SMN1 and SMN2
The SMN1 and SMN2 genes are remarkably similar, differing by only a few nucleotides. The most significant distinction lies in a single nucleotide substitution within exon 7 of the SMN2 gene. This change converts a cytosine (C) to a thymine (T) at position 6, which disrupts a splicing enhancer element.
The SMN1 gene produces a messenger RNA transcript that includes exon 7, resulting in functional SMN protein. In contrast, the C-to-T change in SMN2 causes the cellular machinery to largely skip exon 7 during splicing. This leads to the production of an unstable, truncated protein that is rapidly degraded.
Approximately 85 to 90 percent of the protein produced by SMN2 is the non-functional, truncated form. The remaining 10 to 15 percent of transcripts successfully retain exon 7, creating a small amount of functional, full-length SMN protein. This functional contribution ensures patients lacking SMN1 are not entirely without SMN protein. The more copies of SMN2 a person has, the greater the total amount of residual functional SMN protein available to the motor neurons.
SMN2 Copy Number and Disease Severity
There is no single “normal” number of SMN2 copies, but the count correlates strongly with the level of protection against severe symptoms in patients lacking SMN1 function. The SMN2 copy number is the most reliable predictor of the clinical severity, or phenotype, of SMA.
Patients with a non-functional SMN1 gene and only one or two copies of SMN2 typically present with the most severe forms, such as Type 0 or Type I. Type I SMA is the most common and severe infantile-onset form, characterized by the inability to ever sit without support.
An increase to three copies of SMN2 generally results in an intermediate phenotype, often classified as Type II or Type III SMA. Type II patients can typically sit but cannot walk independently, while Type III patients achieve independent walking at some point.
Individuals with four or more SMN2 copies usually have the mildest forms, such as Type III or Type IV, or may even remain asymptomatic. This higher copy number is protective because the combined output of functional SMN protein is sufficient to prevent significant motor neuron degeneration. However, this correlation is not absolute, and other factors can sometimes lead to a milder or more severe presentation than the copy number alone would predict.
How SMN2 Copies Are Determined
Determining the exact number of SMN2 copies is an important step in diagnosing SMA and informing treatment decisions. Genetic testing is required because SMN1 and SMN2 are so similar that standard gene sequencing cannot easily distinguish between them. Specialized quantitative techniques are necessary to accurately measure the gene dosage.
The most common and reliable methods used in clinical diagnostic laboratories are quantitative Polymerase Chain Reaction (qPCR) and Multiplex Ligation-dependent Probe Amplification (MLPA). Both techniques are designed to quantify the amount of a specific DNA sequence, specifically the sequence unique to SMN2 exon 7.
MLPA utilizes multiple probes that bind to specific target sequences, allowing for the simultaneous detection and quantification of several gene segments, including the region that differentiates SMN1 from SMN2. Quantitative PCR methods, such as TaqMan, use fluorescent probes that specifically target the single nucleotide difference in exon 7 to determine the copy number. These methods compare the signal from the SMN2 gene to a known reference gene to provide a precise count.
Therapeutic Approaches Targeting SMN2
The understanding that SMN2 is a disease modifier has led to the development of effective therapies that directly target this gene. These therapeutic approaches aim to increase the production of full-length, functional SMN protein from the existing SMN2 copies in the patient.
One major class of treatment involves splicing modifiers, which work by correcting the flawed splicing mechanism of the SMN2 gene. Drugs like nusinersen (Spinraza) and risdiplam (Evrysdi) fall into this category. Nusinersen is an antisense oligonucleotide that binds to the SMN2 messenger RNA precursor, blocking the site that causes exon 7 to be skipped. This forces the SMN2 gene to include exon 7, resulting in more full-length, functional SMN protein.
Risdiplam is an orally administered small molecule that works similarly by promoting exon 7 inclusion in the SMN2 transcript. Both treatments leverage the presence of the SMN2 gene, with the patient’s copy number influencing the baseline level of protein that can be boosted. A higher SMN2 copy number provides more genetic templates for these drugs to act upon, which can contribute to a better prognosis.
A different approach is gene replacement therapy, such as onasemnogene abeparvovec (Zolgensma), which bypasses the SMN2 gene entirely. This therapy delivers a functional copy of the SMN1 gene into the motor neurons using a viral vector. While this approach is independent of the SMN2 splicing issue, the patient’s SMN2 copy number remains relevant as it indicates their overall clinical status before treatment initiation.