ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.5827C>T (p.Arg1943Cys) (rs370398704)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000430402 SCV000536633 uncertain significance not provided 2019-06-25 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar but additional evidence is not available (ClinVar Variant ID# 393252; Landrum et al., 2016)
Invitae RCV000477620 SCV000541357 uncertain significance Alstrom syndrome 2019-12-13 criteria provided, single submitter clinical testing This sequence change replaces arginine with cysteine at codon 1944 of the ALMS1 protein (p.Arg1944Cys). The arginine residue is weakly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs370398704, ExAC 0.03%) but has not been reported in the literature in individuals with an ALMS1-related disease. ClinVar contains an entry for this variant (Variation ID: 393252). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a rare missense change with uncertain impact on protein function. Because it is found in the population at an appreciable frequency, this variant is not anticipated to cause disease. However, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.
Natera, Inc. RCV000477620 SCV001455458 likely benign Alstrom syndrome 2019-12-17 no assertion criteria provided clinical testing

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