ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.4068G>A (p.Thr1356=)

gnomAD frequency: 0.01437  dbSNP: rs74714098
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000117840 SCV000170819 benign not specified 2012-05-23 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Laboratory Services, Illumina RCV000473497 SCV000431187 benign Pitt-Hopkins-like syndrome 2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000473497 SCV000562372 benign Pitt-Hopkins-like syndrome 2 2025-02-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV000716687 SCV000847529 benign History of neurodevelopmental disorder 2016-04-15 criteria provided, single submitter clinical testing General population or sub-population frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Breakthrough Genomics, Breakthrough Genomics RCV004707979 SCV005243634 benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000117840 SCV000152110 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
PreventionGenetics, part of Exact Sciences RCV004529972 SCV004729707 benign NRXN1-related disorder 2019-08-12 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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