ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.4004C>T (p.Thr1335Ile) (rs200672080)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000656931 SCV000241926 uncertain significance not provided 2018-04-09 criteria provided, single submitter clinical testing The T1375I variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The T1375I variant is observed in 27/9838 (0.3%) alleles from individuals of Ashkenazi Jewish background in large population cohorts (Lek et al., 2016). The T1375I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, in-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Ambry Genetics RCV000190702 SCV000244143 uncertain significance Inborn genetic diseases 2013-05-10 criteria provided, single submitter clinical testing Insufficient or inconclusive evidence
Illumina Clinical Services Laboratory,Illumina RCV001080620 SCV000431189 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.
Genetic Services Laboratory, University of Chicago RCV000188315 SCV000596061 uncertain significance not specified 2016-02-11 criteria provided, single submitter clinical testing
Invitae RCV001080620 SCV001001921 likely benign Pitt-Hopkins-like syndrome 2 2019-12-31 criteria provided, single submitter clinical testing

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