ClinVar Miner

Submissions for variant NM_001127713.1(ATL1):c.1160T>C (p.Leu387Ser) (rs1595625010)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000816079 SCV000956569 pathogenic Hereditary spastic paraplegia 3A 2018-12-06 criteria provided, single submitter clinical testing This sequence change replaces leucine with serine at codon 387 of the ATL1 protein (p.Leu387Ser). The leucine residue is highly conserved and there is a large physicochemical difference between leucine and serine. This variant is not present in population databases (ExAC no frequency). This variant has been observed to segregate with clinical features of ATL1-related disorder in a family (Invitae) and it has been observed in the literature in an individual affected with hereditary spastic paraplegia (PMID: 26208798). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic.
Mendelics RCV000816079 SCV001139449 likely pathogenic Hereditary spastic paraplegia 3A 2019-05-28 criteria provided, single submitter clinical testing
GeneDx RCV001547425 SCV001767130 uncertain significance not provided 2018-12-19 criteria provided, single submitter clinical testing Reported as an unclassified variant in a patient with hereditary spastic paraplegia (Park et al., 2015); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 26208798)

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