ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.1158+26A>T (rs201802152)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000117834 SCV000152104 uncertain significance not provided 2014-03-24 criteria provided, single submitter clinical testing
GeneDx RCV000188225 SCV000241832 uncertain significance not specified 2017-10-31 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the NRXN1 gene. The c.1278+5 A>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1278+5 A>T variant is observed in 28/7878 (0.4%) alleles from individuals of South Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Several in-silico splice prediction models predict that c.1278+5 A>T has no impact on splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV001083943 SCV000431209 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV001083943 SCV000651807 likely benign Pitt-Hopkins-like syndrome 2 2020-12-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV000719842 SCV000850713 uncertain significance History of neurodevelopmental disorder 2020-03-20 criteria provided, single submitter clinical testing The c.1278+5A>T intronic variant results from an A to T substitution 5 nucleotides after coding exon 7 in the NRXN1 gene. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice donor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Athena Diagnostics Inc RCV000117834 SCV001144778 benign not provided 2018-12-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000117834 SCV001152308 uncertain significance not provided 2018-04-01 criteria provided, single submitter clinical testing
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001251856 SCV001427601 uncertain significance Intellectual disability 2019-01-01 no assertion criteria provided clinical testing

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