Why are SMN1 and SMN2 copy number important and why are they challenging to analyze?
SMN1 and SMN2 are located close to each other at the complex SMN region on chromosome 5q12.2-q13.3 where repetitive sequences, pseudogenes, transposable elements, deletions and inverted duplications are not unusual (PMID: 9950358).
The SMN1 gene (MIM *600354) shares more than 99% nucleotide identity with the SMN2 gene (MIM *601627); both genes encode a 294-amino acid RNA-binding protein, SMN, that is required for efficient assembly of small nuclear ribonucleoprotein (snRNP) complexes.
These two genes, both containing nine exons, can be distinguished only by eight nucleotides (5 intronic and 3 exonic with 1 each located in exons 6, 7, and 8) (PMID: 9950358) making molecular differentiation of these genes extremely difficult.
This case report describes, how the diagnosis of spinal muscular atrophy (SMA) was confirmed for the patient, what testing was chosen, and why the SMN1/SMN2 region is so difficult to sequence.
Patient is a 60-year-old male with spinal muscular atrophy type III diagnosed at the age of 27 years based on electromyoneurography (ENMG) and muscle biopsy findings. The patient presented with symptoms throughout childhood and adolescence including clumsiness while running and difficulty climbing stairs. He is unable to transition independently, has generalized weakened control of body and cervical spine movements, and shortness of breath. There is no known family history of similar disease.
A Blueprint Genetics Spinal Muscular Atrophy Panel was requested which tests for 30 genes including copy number variants and assessment of known disease-causing, deep intronic variants. The Spinal Muscular Atrophy Panel is ideal for patients with a clinical suspicion of distal hereditary motor neuropathy or spinal muscular atrophy. Subsequently, the variant has been reported in additional male patient with X-linked RP (PMID: 28322733). In addition, we have detected the variant in two patients with X-linked retinitis pigmentosa (unpublished observations).
Bioinformatic analysis developed specifically for copy number determination of the SMN1 and SMN2 genes identified a homozygous deletion including at least exon 7 of the SMN1 gene, which is considered as a marker for whole gene deletion. In addition, ≥3 copies of SMN2 were detected. These findings were confirmed using a RNase H2-dependent PCR (rhPCR) developed specifically for SMN copy number analysis. Considering the current literature and well-established role of SMN1 deletions as a disease-causing variant, it was classified as pathogenic.
- The diagnosis of SMA was confirmed.
- Genetic counseling and family member testing are now available to family members to clarify their risk to carry or develop the disease.
- Because the genetic etiology of this patient’s SMA and the number copy number of SMN2 has been identified, they may be eligible to participate in gene therapy clinical trials for patients with multiple copies of SMN2.
Read our white paper The Genetic Horizon – Improving clinical sensitivity in difficult-to-sequence genes for rare hereditary disorders: