ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.206C>T (p.Thr69Met)

gnomAD frequency: 0.00002  dbSNP: rs764422997
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001061175 SCV001225908 uncertain significance Hereditary spastic paraplegia 11 2022-09-23 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 69 of the SPG11 protein (p.Thr69Met). This variant is present in population databases (rs764422997, gnomAD 0.02%). 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: 855832). 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: "Benign"; 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001847142 SCV002105676 uncertain significance Hereditary spastic paraplegia 2019-06-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002418515 SCV002726259 uncertain significance Inborn genetic diseases 2020-08-19 criteria provided, single submitter clinical testing The p.T69M variant (also known as c.206C>T), located in coding exon 1 of the SPG11 gene, results from a C to T substitution at nucleotide position 206. The threonine at codon 69 is replaced by methionine, an amino acid with similar properties. This amino acid position is poorly 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.
Genome-Nilou Lab RCV002468133 SCV002762918 uncertain significance Amyotrophic lateral sclerosis type 5 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002468134 SCV002762919 uncertain significance Charcot-Marie-Tooth disease axonal type 2X criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001061175 SCV002762920 uncertain significance Hereditary spastic paraplegia 11 criteria provided, single submitter clinical testing

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