ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.6071A>G (p.Lys2024Arg) (rs369339997)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000664942 SCV000788983 uncertain significance Alstrom syndrome 2016-12-23 criteria provided, single submitter clinical testing
Invitae RCV000664942 SCV001383492 uncertain significance Alstrom syndrome 2019-09-25 criteria provided, single submitter clinical testing This sequence change replaces lysine with arginine at codon 2025 of the ALMS1 protein (p.Lys2025Arg). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ALMS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 550247). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Not Available"; 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 RCV001449702 SCV001652958 uncertain significance not specified 2020-08-13 criteria provided, single submitter clinical testing The p.Lys2025Arg variant in the ALMS1 gene has not been previously reported in individuals with hearing loss or Alstrom syndrome and was absent from large population studies. This variant has been reported in ClinVar (Variation ID 550247). Computational prediction tools and conservation analysis suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3.

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