ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.3922G>A (p.Glu1308Lys)

dbSNP: rs779198786
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV003237609 SCV002010946 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV002359249 SCV002622070 uncertain significance Inborn genetic diseases 2021-12-16 criteria provided, single submitter clinical testing The p.E1308K variant (also known as c.3922G>A), located in coding exon 23 of the SPG11 gene, results from a G to A substitution at nucleotide position 3922. The glutamic acid at codon 1308 is replaced by lysine, an amino acid with similar properties. This amino acid position is conserved. 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002540739 SCV002971713 uncertain significance Hereditary spastic paraplegia 11 2022-04-28 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1308 of the SPG11 protein (p.Glu1308Lys). This variant is present in population databases (rs779198786, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SPG11-related conditions. ClinVar contains an entry for this variant (Variation ID: 1319615). 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 lysine 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.

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