ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2422G>A (p.Glu808Lys)

gnomAD frequency: 0.00006  dbSNP: rs202145311
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188312 SCV000241923 uncertain significance not provided 2019-04-16 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Missense variant in a gene in which most reported pathogenic variants are truncating/loss-of-function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001852480 SCV002168489 uncertain significance Pitt-Hopkins-like syndrome 2 2022-11-10 criteria provided, single submitter clinical testing This variant is present in population databases (rs202145311, gnomAD 0.003%). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 206278). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 848 of the NRXN1 protein (p.Glu848Lys).

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