A novel SMARCAL1 missense mutation that affects splicing in a severely affected Schimke immunoosseous dysplasia patient

• Published in: European journal of medical genetics Vol. 59; no. 8; pp. 363 - 366
• Main Authors: Barraza-García, Jimena, Rivera-Pedroza, Carlos I, Belinchón, Alberta, Fernández-Camblor, Carlota, Valenciano-Fuente, Blanca, Lapunzina, Pablo, Heath, Karen E
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Masson SAS 01-08-2016
• Subjects: Arteriosclerosis - diagnosis; Arteriosclerosis - genetics; Base Sequence; DNA Helicases - genetics; DNA Mutational Analysis; Gene Order; Genotype; High-Throughput Nucleotide Sequencing; Humans; Immunodeficiency; Immunologic Deficiency Syndromes - diagnosis; Immunologic Deficiency Syndromes - genetics; Infant; Male; Medical Education; Mutation, Missense; Nephropathy; Nephrotic Syndrome - diagnosis; Nephrotic Syndrome - genetics; Osteochondrodysplasias - diagnosis; Osteochondrodysplasias - genetics; Phenotype; Pulmonary Embolism - diagnosis; Pulmonary Embolism - genetics; RNA Splice Sites; RNA Splicing; Severity of Illness Index; SIOD; Skeletal dysplasia; SMARCAL1; SMARCAL1; Nephropathy; Skeletal dysplasia; SIOD; Immunodeficiency
• ISSN: 1769-7212; 1878-0849
• DOI: 10.1016/j.ejmg.2016.06.002

Abstract Schimke immunoosseous dysplasia (SIOD) is an autosomal recessive disease characterized by skeletal dysplasia, focal segmental glomerulosclerosis, renal failure and immunodeficiency. In this work, we report the molecular studies undertaken in a severely affected SIOD patient that died at six years old due to nephropathy. The patient was screened for mutations using a targeted skeletal dysplasias panel. A homozygous novel missense mutation was identified, c.1615C > G (p.[Leu539Val]) that was predicted as mildly pathogenic by in silico pathogenicity prediction tools. However, splicing prediction software suggested that this variant may create a new splicing donor site in exon 9, which was subsequently confirmed using a minigene assay in HEK293 cells. Thus, the splicing alteration, c.1615C > G; r.1615c > g, 1615_1644del; (p.[Leu539_Ile548del]), results in the loss of 10 amino acids of the HARP-ATPase catalytic domain and the RPA-binding domain. Several studies have demonstrated a weak genotype-phenotype correlation among such patients. Thus, the molecular characterization has helped us to understand why a predicted weakly pathogenic missense mutation results in severe SIOD and should be considered in similar scenarios.