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Homozygous deletions of exon 7 in <jats:italic>SMN1<\/jats:italic> result in 95% of SMA cases, while the remaining 5% are caused by other pathogenic variants of <jats:italic>SMN1<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We analyzed two SMA-suspected cases that were collected, with no <jats:italic>SMN1<\/jats:italic> gene deletion and point mutation in whole-exome sequencing. Exon 1 deletion of the <jats:italic>SMN<\/jats:italic> gene was detected using Multiplex ligation-dependent probe amplification (MLPA) P021. We used long-range polymerase chain reaction (PCR) to isolate <jats:italic>the SMN1<\/jats:italic> template, optimized-MLPA P021 for copy number variation (CNV) analysis within <jats:italic>SMN1<\/jats:italic> only, and validated the findings via third-generation sequencing.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Two unrelated families shared a genotype with one copy of exon 7 and a novel variant, g.70919941_70927324del, in isolated exon 1 of the <jats:italic>SMN1<\/jats:italic> gene. Case F1-II.1 demonstrated no exon 1 but retained other exons, whereas F2-II.1 had an exon 1 deletion in a single <jats:italic>SMN1<\/jats:italic> gene. The read coverage in the third-generation sequencing results of both F1-II.1 and F2-II.1 revealed a deletion of approximately 7.3\u00a0kb in the 5\u2019 region of <jats:italic>SMN1<\/jats:italic>. The first nucleotide in the sequence data aligned to the 7385\u00a0bp of NG_008691.1.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Remarkably, two proband families demonstrated identical <jats:italic>SMN1<\/jats:italic> exon 1 breakpoint sites, hinting at a potential novel mutation hotspot in Chinese SMA, expanding the variation spectrum of the <jats:italic>SMN1<\/jats:italic> gene and corroborating the specificity of isolated exon 1 deletion in SMA pathogenesis. The optimized-MLPA P021 determined a novel variant (g.70919941_70927324del) in isolated exon 1 of the <jats:italic>SMN1<\/jats:italic> gene based on long-range PCR, enabling efficient and affordable detection of SMN gene variations in patients with SMA, providing new insight into SMA diagnosis to <jats:italic>SMN1<\/jats:italic> deficiency and an optimized workflow for single exon CNV testing of the <jats:italic>SMN<\/jats:italic> gene.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12883-024-03592-5","type":"journal-article","created":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T05:01:51Z","timestamp":1710133311000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Optimized MLPA workflow for spinal muscular atrophy diagnosis: identification of a novel variant, NC_000005.10:g.(70919941_70927324)del in isolated exon 1 of SMN1 gene through long-range PCR"],"prefix":"10.1186","volume":"24","author":[{"given":"Mei","family":"Yao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liya","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yicheng","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiqin","family":"Cui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuwei","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongming","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6736-1407","authenticated-orcid":false,"given":"Shanshan","family":"Mao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,3,11]]},"reference":[{"key":"3592_CR1","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.molmed.2012.11.002","volume":"19","author":"G Hamilton","year":"2013","unstructured":"Hamilton G, Gillingwater TH. 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