ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.772+1040A>T

gnomAD frequency: 0.00011  dbSNP: rs201741449
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001705029 SCV000241904 likely benign not provided 2020-11-12 criteria provided, single submitter clinical testing
Invitae RCV000691824 SCV000819617 uncertain significance Pitt-Hopkins-like syndrome 2 2024-01-24 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 260 of the NRXN1 protein (p.Lys260Asn). This variant is present in population databases (rs201741449, gnomAD 0.03%). 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: 206261). 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 tolerated. 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 RCV002314735 SCV000849414 uncertain significance Inborn genetic diseases 2021-06-11 criteria provided, single submitter clinical testing The c.780A>T (p.K260N) alteration is located in exon 3 (coding exon 2) of the NRXN1 gene. This alteration results from a A to T substitution at nucleotide position 780, causing the lysine (K) at amino acid position 260 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000691824 SCV001368359 likely benign Pitt-Hopkins-like syndrome 2 2018-10-10 criteria provided, single submitter clinical testing This variant was classified as: Likely benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2.

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