Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency

Abstract

Pathogenic variations in SMPD1 lead to acid sphingomyelinase deficiency (ASMD), that is, Niemann‐Pick disease (NPD) type A and B (NPA, NPB), which is a recessive lysosomal storage disease. The knowledge of variant spectrum in Indian patients is crucial for early and accurate NPD diagnosis and genetic counseling of families. In this study, we recruited 40 unrelated pediatric patients manifesting symptoms of ASMD and subnormal ASM enzyme activity. Variations in SMPD1 were studied using Sanger sequencing for all exons, followed by interpretation of variants based on American College of Medical Genetics and Genomics & Association for Molecular Pathology (ACMG/AMP) criteria. We identified 18 previously unreported variants and 21 known variants, including missense, nonsense, deletions, duplications, and splice site variations with disease‐causing potential. Eight missense variants were functionally characterized using in silico molecular dynamic simulation and in vitro transient transfection in HEK293T cells, followed by ASM enzyme assay, immunoblot, and immunofluorescence studies. All the variants showed reduced ASM activity in transfected cells confirming their disease‐causing potential. The study provides data for efficient prenatal diagnosis and genetic counseling of families with NPD type A and B.

ASM Variants in the Spotlight: A Structure-Based Atlas for Unraveling Pathogenic Mechanisms in Lysosomal Acid Sphingomyelinase

“…The results are supported by experimental assays that reported the ASM C159R 49 and C223S 39 variants with a residual catalytic activity of 8% and 4%, respectively.…”

“…N391H was reported in two infants showing early-onset symptoms classified as Niemann-Pick disease type A 38 . Furthermore, enzymatic activity assays revealed that N391H substantially decreases ASM activity, retaining only 2.61% of the activity observed in the wild type 39 . At the structural level, N391 is highly buried to the solvent (SASA LJ 0%), and its side chain forms hydrogen bonds with the main chain of F329 (46% in MD frames) and N385 (35% in MD frames, Table S4 ).…”

“…Of these, experimental data confirmed a mild effect on the catalytic activity (50-70% of residual activity) for A487V and V314M ( Table S3 ), strongly supporting that these variants alone could be connected to benign or very mild phenotypes 48,50 . On the contrary, R202H was shown with a drastic reduction of activity (< 5 %, Table S3 ) 39 , and further experimental and structural studies would be needed to understand its effect. At the structural level, it is located at a distal site from the catalytic site and the region of interaction with the membrane.…”

SMPD1 gene variants in patients with β-Thalassemia major

“…A strong correlation exists between SMPD1 gene variants and L-ASM levels, and these gene variants are detected in patients with NPD [ 25 , 26 ], as in the case of an 11-year-old patient with NPD with a rare mutation in SMPD1 [ 27 ]. However, no such studies have been conducted in patients with β-TM.…”

Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases

“…Sphingolipidoses are characterized by abnormal storage of various phospholipids with a sphingosine group, and include: Fabry ( GLA ), Niemann–Pick A/B ( SMPD1 ), Krabbe ( GALC ), Gaucher ( GBA ), Tay–Sachs ( HEXA ), Farber ( ASAH1 ), Sandhoff ( HEXB ) and Metachromatic Leukodystrophy ( ARSA ) [ 2 ]. A number of disease-causing gene CNVs have been described, including: (i) a gross deletion involving ASAH1 (g.728_18197del (c.126-3941_382 + 1358del) in a child with severe Farber disease [ 21 ]; (ii) a whole-gene deletion of ARSA in a patient with infantile Metachromatic Leukodystrophy [ 22 ]; (iii) two single-exon deletion involving GALC exon 12 and 14 and multiple contiguous exons loss (exons 11–17) in patients with Krabbe disease [ 23 ]; (iv) a recurrent 5′-end 16 kb deletion comprising HEXB promoter region, exons 1–5 and part of intron 5 in Sandhoff disease patients [ 24 , 25 ], and further partial deletions comprising intron 1-exon 2 [ 25 ] and exons 1–5 [ 26 ]; (v) multiple complex pathogenic duplications or deletions of SMPD1 in patients with acid sphingomyelinase deficiency [ 27 ].…”