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

gnomAD frequency: 0.01437  dbSNP: rs74714098

Total submissions: 7

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).