ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2605C>A (p.Leu869Met)

gnomAD frequency: 0.00044  dbSNP: rs201818223
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000723597 SCV000111399 uncertain significance not provided 2013-03-08 criteria provided, single submitter clinical testing
GeneDx RCV000723597 SCV000241892 likely benign not provided 2021-02-09 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000188281 SCV000248282 uncertain significance not specified 2015-06-24 criteria provided, single submitter clinical testing
Invitae RCV001085353 SCV000286214 benign Pitt-Hopkins-like syndrome 2 2023-12-22 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001085353 SCV000431202 uncertain significance Pitt-Hopkins-like syndrome 2 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Fulgent Genetics, Fulgent Genetics RCV000515261 SCV000611416 uncertain significance Pitt-Hopkins-like syndrome 2; Chromosome 2p16.3 deletion syndrome 2017-05-23 criteria provided, single submitter clinical testing
Ambry Genetics RCV002316229 SCV000850741 uncertain significance Inborn genetic diseases 2019-04-04 criteria provided, single submitter clinical testing The p.L909M variant (also known as c.2725C>A), located in coding exon 14 of the NRXN1 gene, results from a C to A substitution at nucleotide position 2725. The leucine at codon 909 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004537324 SCV004750083 benign NRXN1-related disorder 2019-07-02 criteria provided, single submitter 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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