ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2815G>A (p.Asp939Asn)

gnomAD frequency: 0.00004  dbSNP: rs796052781
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188284 SCV000241895 uncertain significance not provided 2015-08-21 criteria provided, single submitter clinical testing The D979N 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 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The D979N 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 highly conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. However, missense mutations in nearby residues have not been reported. 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 EPILEPSY panel(s).
CeGaT Center for Human Genetics Tuebingen RCV000188284 SCV001746357 uncertain significance not provided 2021-04-01 criteria provided, single submitter clinical testing
Invitae RCV001857626 SCV002120009 uncertain significance Pitt-Hopkins-like syndrome 2 2023-12-08 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 979 of the NRXN1 protein (p.Asp979Asn). This variant is present in population databases (rs796052781, gnomAD 0.02%). 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: 206253). 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.

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