ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2459G>A (p.Ser820Asn) (rs80293130)

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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 RCV000720544 SCV000851423 uncertain significance History of neurodevelopmental disorder 2016-12-20 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000728599 SCV000856192 uncertain significance not provided 2017-08-23 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515422 SCV000611415 uncertain significance Pitt-Hopkins-like syndrome 2; Schizophrenia 17 2017-05-23 criteria provided, single submitter clinical testing
GeneDx RCV000188271 SCV000241881 likely benign not specified 2017-12-20 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.
Genetic Services Laboratory, University of Chicago RCV000188271 SCV000248279 uncertain significance not specified 2014-07-18 criteria provided, single submitter clinical testing
Invitae RCV000706193 SCV000835231 uncertain significance Pitt-Hopkins-like syndrome 2 2018-12-01 criteria provided, single submitter clinical testing This sequence change replaces serine with asparagine at codon 860 of the NRXN1 protein (p.Ser860Asn). The serine residue is highly conserved and there is a small physicochemical difference between serine and asparagine. This variant is present in population databases (rs80293130, ExAC 0.06%). This variant has not been reported in the literature in individuals with NRXN1-related disease. ClinVar contains an entry for this variant (Variation ID: 206242). 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.

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