Description
The p.Phe333SerfsTer52 variant in SMPD1 (also known as p.Phe331SerfsTer52 due to a difference in cDNA numbering) has been reported in at least 9 individuals with Niemann-Pick disease, segregated with disease in 3 individuals from 1 family (PMID: 15877209, 9266408, 29995201, 8401540, 12369017), and has been identified in 0.129% (13/10078) of Ashkenazi Jewish chromosomes and 0.001% (1/113702) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs387906289). Although this variant has been seen in the general population, its frequency is consistent with the increased carrier rate in the Ashkenazi Jewish population and is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (VariationID: 2990) as pathogenic by Counsyl, EGL Genetic Diagnostics, GeneReviews, Integrated Genetics, and OMIM. In vitro functional studies provide some evidence that the p.Phe333Serfs variant may impact protein function (PMID: 15877209; 9266408). However, these types of assays may not accurately represent biological function. This variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at position 333 and leads to a premature termination codon 52 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Although this variant causes loss of function, it is pathogenic without the use of PVS1 and was used to establish whether loss of function is a mechanism of disease. The phenotype of individuals compound heterozygous for this variant is highly specific for Niemann-Pick disease based on acid sphingomyelinase activity being <10%, consistent with disease (PMID: 15877209). The presence of this variant in combination with reported pathogenic or likely pathogenic variants in at least 7 individuals with Niemann-Pick disease increases the likelihood that the p.Phe333Serfs variant is pathogenic (VariationID: 198093, 2980; PMID: 15877209, 9266408, 29995201, 8401540, 12369017). In summary, this variant meets criteria to be classified as pathogenic for Niemann-Pick disease in an autosomal recessive manner based on its presence in trans with other pathogenic variants in affected individuals, in vitro functional studies, cosegregation, and the phenotype of patients with the variant being highly specific for disease. ACMG/AMP Criteria applied: PM3_very-strong, PS3_moderate, PP1, PP4 (Richards 2015).
| # | Sample | Method | Observation |
|---|
| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
|---|
| 1 | germline | unknown | not provided | not provided | not provided | | not provided | not provided | not provided | not provided |
