Submissions for variant NM_001330078.2(NRXN1):c.3375A>G (p.Thr1125=)

gnomAD frequency: 0.00001  dbSNP: rs757748286

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000604096	SCV000728014	likely benign	not specified	2018-03-06	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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000924784	SCV001070306	likely benign	Pitt-Hopkins-like syndrome 2	2024-08-31	criteria provided, single submitter	clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV003224348	SCV003920302	uncertain significance	Pitt-Hopkins-like syndrome 2; Chromosome 2p16.3 deletion syndrome	2021-03-30	criteria provided, single submitter	clinical testing	NRXN1 NM_001135659 exon 19 p.Thr1165Thr (c.3495A>G): This variant has not been reported in the literature but is present in 2/33456 Latino individuals in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs757748286). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.