ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.4580A>G (p.Asn1527Ser) (rs145038571)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000718427 SCV000849290 likely benign Seizures 2017-04-04 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Subpopulation frequency in support of benign classification
Athena Diagnostics Inc RCV000713515 SCV000844136 likely benign not provided 2018-07-10 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000713515 SCV000229775 uncertain significance not provided 2014-07-16 criteria provided, single submitter clinical testing
GeneDx RCV000189464 SCV000243105 likely benign not specified 2017-10-31 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Clinical Services Laboratory,Illumina RCV000294244 SCV000477513 likely benign Early Infantile Epileptic Encephalopathy, Autosomal Dominant 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000468476 SCV000553149 uncertain significance Early infantile epileptic encephalopathy 2018-05-12 criteria provided, single submitter clinical testing This sequence change replaces asparagine with serine at codon 1527 of the SPTAN1 protein (p.Asn1527Ser). The asparagine residue is moderately conserved and there is a small physicochemical difference between asparagine and serine. This variant is present in population databases (rs145038571, ExAC 0.07%), 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: 196941). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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