ClinVar Miner

Submissions for variant NM_001040436.3(YARS2):c.202G>A (p.Gly68Ser)

gnomAD frequency: 0.00009  dbSNP: rs150304121
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000195740 SCV000252565 likely benign not specified 2013-11-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Laboratory Services, Illumina RCV001113499 SCV001271278 uncertain significance Myopathy, lactic acidosis, and sideroblastic anemia 2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV002517283 SCV003493689 uncertain significance not provided 2022-10-01 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 68 of the YARS2 protein (p.Gly68Ser). This variant is present in population databases (rs150304121, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with YARS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 215418). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt YARS2 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Revvity Omics, Revvity RCV001113499 SCV003823841 uncertain significance Myopathy, lactic acidosis, and sideroblastic anemia 2 2021-10-01 criteria provided, single submitter clinical testing

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