ClinVar Miner

Submissions for variant NM_018418.5(SPATA7):c.1035G>A (p.Met345Ile)

gnomAD frequency: 0.00001  dbSNP: rs764902056
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001760741 SCV001990509 uncertain significance not provided 2019-08-08 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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
Labcorp Genetics (formerly Invitae), Labcorp RCV002544028 SCV003484540 uncertain significance Leber congenital amaurosis 3 2022-06-27 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 345 of the SPATA7 protein (p.Met345Ile). 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1307323). This variant has not been reported in the literature in individuals affected with SPATA7-related conditions. This variant is present in population databases (rs764902056, gnomAD 0.002%).

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