ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.152A>T (p.Asp51Val)

gnomAD frequency: 0.00001  dbSNP: rs748589919
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genome-Nilou Lab RCV001579137 SCV001806555 uncertain significance Niemann-Pick disease, type A 2021-07-22 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001579138 SCV001806556 uncertain significance Niemann-Pick disease, type B 2021-07-22 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV003136114 SCV003822008 uncertain significance not provided 2019-05-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003235590 SCV003934636 likely pathogenic Sphingomyelin/cholesterol lipidosis 2023-05-16 criteria provided, single submitter clinical testing Variant summary: SMPD1 c.152A>T (p.Asp51Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 249640 control chromosomes. c.152A>T has been reported in the literature in individuals affected with Niemann-Pick Disease (Simonaro_2002, Wasserstein_2006), and these patients were reported as compound heterozygous with variants that may be pathogenic. These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 12369017, 17011332). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV001579137 SCV004203210 likely pathogenic Niemann-Pick disease, type A 2023-11-18 criteria provided, single submitter clinical testing

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