ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2623A>G (p.Asn875Asp)

gnomAD frequency: 0.00001  dbSNP: rs201243629
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001222195 SCV001394285 uncertain significance Pitt-Hopkins-like syndrome 2 2023-10-22 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 915 of the NRXN1 protein (p.Asn915Asp). This variant is present in population databases (rs201243629, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 950477). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
Ambry Genetics RCV002436861 SCV002749421 uncertain significance Inborn genetic diseases 2017-10-30 criteria provided, single submitter clinical testing The p.N915D variant (also known as c.2743A>G), located in coding exon 14 of the NRXN1 gene, results from an A to G substitution at nucleotide position 2743. The asparagine at codon 915 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV002511059 SCV002822655 uncertain significance not provided 2022-10-01 criteria provided, single submitter clinical testing NRXN1: PP3
GeneDx RCV002511059 SCV004169943 uncertain significance not provided 2023-05-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; 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

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