ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2507C>T (p.Ala836Val) (rs199557987)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000174865 SCV000226251 likely benign not specified 2015-01-30 criteria provided, single submitter clinical testing
GeneDx RCV000174865 SCV000241885 uncertain significance not specified 2013-07-14 criteria provided, single submitter clinical testing The Ala876Val missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Ala876Val is a conservative amino acid substitution as both Alanine and Valine are uncharged, non-polar residues. The variant occurs at a position in the fourth lamin G domain of the protein that is conserved through mammals. Two in silico algorithms predict that Ala876Val is benign, while another algorithm predicts that the variant is damaging to the structure/function of the protein. Therefore, based on the currently available information, it is unclear whether Ala876Val is a disease-causing mutation or a rare benign variant. The variant is found in EPILEPSY panel(s).
Genetic Services Laboratory, University of Chicago RCV000174865 SCV000248280 uncertain significance not specified 2015-06-23 criteria provided, single submitter clinical testing
Invitae RCV000868228 SCV001009532 likely benign Pitt-Hopkins-like syndrome 2 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000868228 SCV001302025 likely benign 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 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.

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