ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.3479A>G (p.Gln1160Arg)

gnomAD frequency: 0.00001  dbSNP: rs768319291
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188299 SCV000241910 uncertain significance not provided 2014-03-12 criteria provided, single submitter clinical testing The Q1200R variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these population. The Q1200R variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is not conserved across species, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in INFANT-EPI panel(s).
Labcorp Genetics (formerly Invitae), Labcorp RCV002514023 SCV002941766 uncertain significance Pitt-Hopkins-like syndrome 2 2022-02-28 criteria provided, single submitter clinical testing 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: 206266). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. This variant is present in population databases (rs768319291, gnomAD 0.002%). This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 1200 of the NRXN1 protein (p.Gln1200Arg).

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