Niemann-Pick Disease Types A and B via the SMPD1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
472 SMPD1$750.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
This test detects ~99% of SMPD1 mutations (McGovern, M.M. and Schuchman, E. H. GeneReviews, 2009).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 SMPD1$990.00 81479 Add to Order
Pricing Comment

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Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity
Thus far, no gross deletions or duplications have been reported in SMPD1 (Human Gene Mutation Database).

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Clinical Features
Niemann-Pick Disease (NPD) is one of several disorders of sphingolipid metabolism known as sphingolipidoses. NPD Types A and B (NPD-A and NPD-B) both result from deficient activity of acid-sphingomyelinase (ASM) and subsequent accumulation of sphingomyelin and other lipids in tissues. NPD-A and B are differentiated based on the age of onset, progression and clinical features.

NPD-A is a uniformly fatal neurodegenerative disease with onset before the age of 6 months and death by the age of 3 years. The clinical hallmarks of NPD-A are hepatosplenomegaly, cherry-red maculae, failure to thrive, hypotonia, and severe psychomotor retardation.

NPD-B is heterogeneous. Symptoms may begin in early childhood or adulthood and progression rate varies among affected individuals, with survival into adulthood. Clinical features of NPD-B may include hepatosplenomegaly, hematological findings, frequent respiratory infections and growth retardation. There is little or no central nervous involvement in NPD-B (Schuchman et al. In: Scriver et al. eds. The Metabolic and Molecular Bases of Inherited Disease. 8th ed.:3589–3610, 2001).

ASM deficiency affects ~ 1:250,000 individuals (Meikle et al. JAMA 281(3):249-254, 1999).  Both forms of the disease arise worldwide with high incidence in individuals of Turkish, Saudi and North African origins; however, the incidence of NPD-A is highest in Ashkenazi Jewish populations (Simonaro et al. Am J Hum Genet 71(6):1413-1419, 2002).
NPD-A and B are inherited in an autosomal recessive manner and result from mutations in the SMPD1 gene (Levran et al. Proc Natl Acad Sci USA 88(9):3748-3752, 1991). SMPD1 encodes the ASM, which catalyzes the hydrolysis of sphingomyelin to phosphorylcholine and ceramide. Although over 160 mutations distributed along the gene have been detected in patients with NPD-A and B, four common mutations have been reported. Three of these mutations (Leu304Pro, Arg498Leu and Phe333Serfs*52) account for ~ 95% of patients with NPD-A, and one recurrent mutation, Arg608del, is responsible for most cases of NPD-B of Ashkenazi Jewish origin (Schuchman and Miranda. Genet Test 1(1):13-19, 1997). The majority of mutations are missense. However, nonsense, splicing, small insertions or deletions have been reported. To date, no pathogenic regulatory variants or large deletions have been reported.

Heterozygous carrier individuals may develop NPD-B (Lee et al. Hum Genet 112(5-6):552-562, 2003) and paternal imprinting at the SMPD1 gene has been reported (Simonaro  Am J Hum Genet 78(5): 865-870, 2006).
Testing Strategy
This test involves bidirectional DNA Sanger sequencing of all coding exons and splice sites of the SMPD1 gene. The full coding sequence of each exon plus ~10 bp of flanking DNA on either side are sequenced. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
Patients with NPD-A and NPD-B and heterozygous carrier relatives.


Official Gene Symbol OMIM ID
SMPD1 607608
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Genetic Counselors
  • Human Gene Mutation Database (Bio-base).
  • Lee, C. Y. (2003). "Compound heterozygosity at the sphingomyelin phosphodiesterase-1 (SMPD1) gene is associated with low HDL cholesterol." Hum Genet 112(5-6): 552-562. PubMed ID: 12607113
  • Levran, O., (1991). "Niemann-Pick disease: a frequent missense mutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients." Proc Natl Acad Sci U S A 88(9): 3748-3752. PubMed ID: 2023926
  • McGovern, M. M. and Schuchman, E.H. (2009). "Acid Sphingomyelinase Deficiency." GeneReviews. PubMed ID: 20301544
  • Meikle, P. J. (1999). "Prevalence of lysosomal storage disorders." JAMA 281(3): 249-254. PubMed ID: 9918480
  • Schuchman et al. In: Scriver et al. eds. The Metabolic and Molecular Bases of Inherited Disease. 8th ed.:3589–3610, 2001.
  • Schuchman, E. H. and Miranda, S. R. (1997). "Niemann-Pick disease: mutation update, genotype/phenotype correlations, and prospects for genetic testing." Genet Test 1(1): 13-19. PubMed ID: 10464620
  • Simonaro, C. M. (2006). "Imprinting at the SMPD1 locus: implications for acid sphingomyelinase-deficient Niemann-Pick disease." Am J Hum Genet 78(5): 865-870. PubMed ID: 16642440
  • Simonaro, C. M., (2002). "The demographics and distribution of type B Niemann-Pick disease: novel mutations lead to new genotype/phenotype correlations." Am J Hum Genet 71(6): 1413-1419. PubMed ID: 12369017
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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