Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Counsyl | RCV000411564 | SCV000486483 | likely pathogenic | Niemann-Pick disease, type A | 2016-06-08 | criteria provided, single submitter | clinical testing | |
| Invitae | RCV001067896 | SCV001232979 | pathogenic | Niemann-Pick disease, type B; Niemann-Pick disease, type A | 2023-08-16 | criteria provided, single submitter | clinical testing | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 371029). This premature translational stop signal has been observed in individual(s) with acid sphingomyelinase-deficient Niemann-Pick disease (PMID: 24718843). This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Asp51Leufs*25) in the SMPD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SMPD1 are known to be pathogenic (PMID: 12369017, 15221801). |
| Broad Center for Mendelian Genomics, |
RCV000411564 | SCV001422717 | pathogenic | Niemann-Pick disease, type A | 2020-01-22 | criteria provided, single submitter | curation | The p.Asp51LeufsTer25 variant in SMPD1 (also known as p.Asp49LeufsTer25 due to a difference in cDNA numbering) has been reported in one Cambodian individual with Niemann-Pick disease (PMID: 24718843) and has been identified in 0.006% (1/15898) of African chromosomes and 0.001% (1/112280) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1057516949). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (VariationID: 371029) as likely pathogenic by Counsyl. This variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at position 51 and leads to a premature termination codon 25 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the SMPD1 gene is an established disease mechanism in autosomal recessive Niemann-Pick disease. The phenotype of an individual compound heterozygous for this variant is highly specific for Niemann-Pick disease based on acid sphingomyelinase activity being <10% of normal, consistent with disease (PMID: 24718843). In summary, this variant meets criteria to be classified as pathogenic for Niemann-Pick disease in an autosomal recessive manner based on the prediction that it will cause loss of function, the phenotype of an individual with the variant being highly specific for disease, and the low frequency of the variant in the general population. ACMG/AMP Criteria applied: PVS1, PM2, PP4 (Richards 2015). |
| Baylor Genetics | RCV000411564 | SCV004203220 | pathogenic | Niemann-Pick disease, type A | 2023-09-07 | criteria provided, single submitter | clinical testing |