ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1675G>A (p.Val559Ile)

gnomAD frequency: 0.00051  dbSNP: rs149939736
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000732105 SCV000860011 uncertain significance not provided 2018-03-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001245456 SCV001418746 likely benign Niemann-Pick disease, type B; Niemann-Pick disease, type A 2024-07-19 criteria provided, single submitter clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000732105 SCV002009083 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001245456 SCV002792080 uncertain significance Niemann-Pick disease, type B; Niemann-Pick disease, type A 2021-10-22 criteria provided, single submitter clinical testing
GeneDx RCV000732105 SCV005401478 uncertain significance not provided 2025-01-03 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV001766586 SCV002092294 uncertain significance Niemann-Pick disease, type A 2017-11-17 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003938115 SCV004753098 uncertain significance SMPD1-related disorder 2024-01-24 no assertion criteria provided clinical testing The SMPD1 c.1675G>A variant is predicted to result in the amino acid substitution p.Val559Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.090% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Of note, a different variant impacting the same amino acid (p.Val559Leu) has been reported in the compound heterozygous state in a patient with sphingomyelinase deficiency and measurement of acid sphingomyelinase activity was supportive of a mild defect (Patient 18, Zhang et al. 2013. PubMed ID: 23356216). At this time, the clinical significance of the c.1675G>A (p.Val559Ile) variant is uncertain due to the absence of conclusive functional and genetic evidence.

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