ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.11584T>C (p.Ser3862Pro) (rs202227966)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000481715 SCV000573749 uncertain significance not provided 2021-08-12 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 423980; Landrum et al., 2016)
Invitae RCV000704301 SCV000833245 uncertain significance Alstrom syndrome 2019-12-19 criteria provided, single submitter clinical testing This sequence change replaces serine with proline at codon 3863 of the ALMS1 protein (p.Ser3863Pro). The serine residue is highly conserved and there is a moderate physicochemical difference between serine and proline. This variant is present in population databases (rs202227966, ExAC 0.2%). This variant has not been reported in the literature in individuals with ALMS1-related disease. ClinVar contains an entry for this variant (Variation ID: 423980). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; Align-GVGD: "Class C0". In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000825863 SCV000967348 uncertain significance not specified 2018-09-17 criteria provided, single submitter clinical testing The p.Ser3863Pro variant in ALMS1 has not been previously reported in individual s with hearing loss or Alstrom syndrome but has been identified in 0.18% (44/240 14) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gn omad.broadinstitute.org). This variant has been reported in ClinVar (Variation ID 406025). Computational prediction tools and conservation analysis do not prov ide strong support for or against an impact to the protein. In summary, the clin ical significance of the p.Ser3863Pro variant is uncertain. ACMG/AMP Criteria ap plied: BS1_Supporting.

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