ClinVar Miner

Submissions for variant NM_001127713.1(ATL1):c.467C>T (p.Thr156Ile) (rs137852657)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota RCV000020721 SCV000840442 pathogenic Hereditary spastic paraplegia 3A 2017-01-13 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000713455 SCV000844063 pathogenic not provided 2018-07-26 criteria provided, single submitter clinical testing
Invitae RCV000020721 SCV001214079 pathogenic Hereditary spastic paraplegia 3A 2019-04-05 criteria provided, single submitter clinical testing This sequence change replaces threonine with isoleucine at codon 156 of the ATL1 protein (p.Thr156Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has been observed to segregate with hereditary spastic paraplegia in a family (PMID: 15477516). ClinVar contains an entry for this variant (Variation ID: 21531). 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.
GeneReviews RCV000020721 SCV000041291 pathologic Hereditary spastic paraplegia 3A 2010-09-21 no assertion criteria provided curation Converted during submission to Pathogenic.

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