ClinVar Miner

Submissions for variant NM_002109.6(HARS1):c.1519T>C (p.Cys507Arg)

gnomAD frequency: 0.00001  dbSNP: rs150090766
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001361381 SCV001557356 uncertain significance Usher syndrome type 3B 2023-10-04 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 507 of the HARS protein (p.Cys507Arg). This variant is present in population databases (rs150090766, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with HARS-related conditions. ClinVar contains an entry for this variant (Variation ID: 1053083). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
GeneDx RCV001776221 SCV002012605 uncertain significance not provided 2019-05-17 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
Ambry Genetics RCV002462955 SCV002756349 uncertain significance Inborn genetic diseases 2020-01-18 criteria provided, single submitter clinical testing The p.C507R variant (also known as c.1519T>C), located in coding exon 13 of the HARS gene, results from a T to C substitution at nucleotide position 1519. The cysteine at codon 507 is replaced by arginine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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