ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)

dbSNP: rs1422720020
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000668954 SCV000793638 likely pathogenic Niemann-Pick disease, type A 2017-08-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001380610 SCV001578730 pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-04-11 criteria provided, single submitter clinical testing The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 553487). This premature translational stop signal has been observed in individual(s) with Niemann-Pick disease (PMID: 23356216, 27338287). This sequence change creates a premature translational stop signal (p.Phe368Valfs*23) 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).
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001380610 SCV001870419 pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A criteria provided, single submitter clinical testing A single base pair insertion in exon 3 of the SMPD1 gene that results in a frameshift and premature truncation of the protein 23 amino acids downstream to codon 368 was detected The observed variant c.1101dup (p.Phe368ValfsTer23) has not been reported in the 1000 genomes and ExAC databases. The in silico prediction of the variant is damaging by MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as pathogenic.
Baylor Genetics RCV000668954 SCV005052841 pathogenic Niemann-Pick disease, type A 2024-03-11 criteria provided, single submitter clinical testing

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