ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.1689G>T (p.Met563Ile) (rs373973880)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189434 SCV000243074 uncertain significance not specified 2014-06-10 criteria provided, single submitter clinical testing The variant is found in INFANT-EPI panel(s).
Invitae RCV000699799 SCV000828526 uncertain significance Early infantile epileptic encephalopathy 2018-08-02 criteria provided, single submitter clinical testing This sequence change replaces methionine with isoleucine at codon 563 of the SPTAN1 protein (p.Met563Ile). The methionine residue is moderately conserved and there is a small physicochemical difference between methionine and isoleucine. This variant is present in population databases (rs373973880, ExAC 0.01%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has not been reported in the literature in individuals with SPTAN1-related disease. ClinVar contains an entry for this variant (Variation ID: 207264). 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 tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Athena Diagnostics Inc RCV000713504 SCV000844125 uncertain significance not provided 2018-02-09 criteria provided, single submitter clinical testing

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