ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.5077G>A (p.Ala1693Thr)

gnomAD frequency: 0.00001  dbSNP: rs753244084
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001036758 SCV001200138 uncertain significance Hereditary spastic paraplegia 11 2021-12-25 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1693 of the SPG11 protein (p.Ala1693Thr). This variant is present in population databases (rs753244084, gnomAD 0.003%). 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: 835790). 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: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Ambry Genetics RCV002337092 SCV002642905 uncertain significance Inborn genetic diseases 2019-11-12 criteria provided, single submitter clinical testing The p.A1693T variant (also known as c.5077G>A), located in coding exon 29 of the SPG11 gene, results from a G to A substitution at nucleotide position 5077. The alanine at codon 1693 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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