Submissions for variant NM_000543.5(SMPD1):c.538_539del (p.Leu180fs)

dbSNP: rs786204694

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Counsyl	RCV000169504	SCV000220967	likely pathogenic	Niemann-Pick disease, type A	2014-12-18	criteria provided, single submitter	literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000169504	SCV000697416	pathogenic	Niemann-Pick disease, type A	2017-05-22	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV001067762	SCV001232841	pathogenic	Niemann-Pick disease, type B; Niemann-Pick disease, type A	2023-11-14	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Leu180Alafs*12) 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). This variant is present in population databases (rs746454813, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with clinical features of acid sphingomyelinase deficiency (PMID: 1618760). This variant is also known as fsL178. ClinVar contains an entry for this variant (Variation ID: 189096). For these reasons, this variant has been classified as Pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV001248975	SCV001422816	pathogenic	Sphingomyelin/cholesterol lipidosis	2020-01-22	criteria provided, single submitter	curation	The p.Leu180AlafsTer12 variant in SMPD1 (also known as p.Leu178AlafsTer12 due to a difference in cDNA numbering) has been reported in at least 2 individuals with Niemann-Pick disease (PMID: 15877209, 1618760) and has been identified in 0.003% (4/117524) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs786204694). 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: 189096) as likely pathogenic by Counsyl and as pathogenic by Integrated Genetics. In vitro functional studies provide some evidence that the p.Leu180AlafsTer12 variant may impact protein function (PMID: 26499107, 1618760). 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 180 and leads to a premature termination codon 2 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the SMPD1 gene is a moderately established disease mechanism in autosomal recessive Niemann-Pick disease. The presence of this variant in 1 affected homozygote and in combination with a reported pathogenic variant in an individual with Niemann-Pick disease increases the likelihood that the p.Leu180AlafsTer12 variant is pathogenic (VariationID: 2896; PMID: 15877209). The phenotype of individuals homozygous and 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: 1618760, 15877209). 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 causes loss of function, functional studies, and the presence of the variant in an affected homozygote and compound heterozygote. ACMG/AMP Criteria applied: PVS1, PS3, PM2, PM3, PP4 (Richards 2015).
Baylor Genetics	RCV000169504	SCV004203224	pathogenic	Niemann-Pick disease, type A	2024-03-12	criteria provided, single submitter	clinical testing
OMIM	RCV000169504	SCV000023277	pathogenic	Niemann-Pick disease, type A	1992-01-01	no assertion criteria provided	literature only
Natera, Inc.	RCV000169504	SCV002091682	pathogenic	Niemann-Pick disease, type A	2017-03-17	no assertion criteria provided	clinical testing