Epidemiological, clinical and biochemical characterization of the p.(Ala359Asp) SMPD1 variant causing Niemann-Pick disease type B.
Niemann-Pick disease type B (NPDB) is a rare, inherited lysosomal storage disorder that occurs due to variants in the sphingomyelin phosphodiesterase 1 (SMPD1) gene and the resultant deficiency of acid sphingomyelinase (ASM) activity. While numerous variants causing NPDB have been described, only a small number have been studied in any detail. Herein, we describe the frequency of the p.(Ala359Asp) variant in the healthy Chilean population, and determine the haplotype background of homozygous patients to establish if this variant originated from a common founder. Genomic DNA samples from 1691 healthy individuals were analyzed for the p.(Ala359Asp) variant. The frequency of p.(Ala359Asp) was found to be 1/105.7, predicting a disease incidence of 1/44 960 in Chile, higher than the incidence estimated by the number of confirmed NPDB cases. We also describe the clinical characteristics of 13 patients homozygous for p.(Ala359Asp) and all of them had moderate to severe NPDB disease. In addition, a conserved haplotype and shared 280 Kb region around the SMPD1 gene was observed in the patients analyzed, indicating that the variant originated from a common ancestor. The haplotype frequency and mitochondrial DNA analysis suggest an Amerindian origin for the variant. To assess the effect of the p.(Ala359Asp) variant, we transfected cells with the ASM-p.(Ala359Asp) cDNA and the activity was only 4.2% compared with the wild-type cDNA, definitively demonstrating the causative effect of the variant on ASM function. Information on common variants such as p.(Ala359Asp) is essential to guide the successful implementation for future therapies and benefit to patients.
Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.|FONDAP Center for Genome Regulation (CGR), Santiago, Chile.
Mariana
M
Acuña
Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.|FONDAP Center for Genome Regulation (CGR), Santiago, Chile.
Pablo
P
Martínez
FONDAP Center for Genome Regulation (CGR), Santiago, Chile.|Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
Carol
C
Moraga
Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Xingxuan
X
He
Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
Mauricio
M
Moraga
Hospital Luis Calvo Mackenna, Santiago, Chile.
Bessie
B
Hunter
Cologne Center for Genomics (CCG), University of Cologne, Köln, Germany.
Peter
P
Nuernberg
FONDAP Center for Genome Regulation (CGR), Santiago, Chile.|Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
Rodrigo A
RA
Gutiérrez
FONDAP Center for Genome Regulation (CGR), Santiago, Chile.|INTA, Universidad de Chile, Santiago, Chile.
Mauricio
M
González
Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Edward H
EH
Schuchman
Departamento de Nutrición, Pontificia Universidad Católica de Chile, Santiago, Chile.
José Luis
JL
Santos
Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.|FONDAP Center for Genome Regulation (CGR), Santiago, Chile.
Juan Francisco
JF
Miquel
Hospital Dr. Exequiel González Cortés, Unidad de Neurología, Santiago, Chile.
Paulina
P
Mabe
Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.|FONDAP Center for Genome Regulation (CGR), Santiago, Chile.
Silvana
S
Zanlungo
D002677:Chile / Q000453:epidemiology; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D018703:Founder Effect; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008875:Middle Aged; D009154:Mutation; D052537:Niemann-Pick Disease, Type B / Q000453:epidemiology / Q000235:genetics*; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D013108:Sphingomyelin Phosphodiesterase / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*
D004272:DNA, Mitochondrial; C543066:SMPD1 protein, human; D013108:Sphingomyelin Phosphodiesterase