ClinVar Miner

Submissions for variant NM_003119.4(SPG7):c.4G>A (p.Ala2Thr) (rs535030441)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000197390 SCV000252311 likely benign not specified 2017-09-15 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.
Athena Diagnostics Inc RCV000197390 SCV000615439 uncertain significance not specified 2016-12-31 criteria provided, single submitter clinical testing
Invitae RCV000817246 SCV000957796 uncertain significance Spastic paraplegia 7 2018-07-27 criteria provided, single submitter clinical testing This sequence change replaces alanine with threonine at codon 2 of the SPG7 protein (p.Ala2Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. While this variant is present in population databases (rs535030441), the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with SPG7-related disease. ClinVar contains an entry for this variant (Variation ID: 215198). 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.

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