ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.2597T>C (p.Ile866Thr)

dbSNP: rs796052779
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188280 SCV000241891 uncertain significance not provided 2020-03-06 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000538380 SCV000651817 uncertain significance Pitt-Hopkins-like syndrome 2 2022-09-10 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 206250). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 906 of the NRXN1 protein (p.Ile906Thr).
Fulgent Genetics, Fulgent Genetics RCV002492865 SCV002782280 uncertain significance Pitt-Hopkins-like syndrome 2; Chromosome 2p16.3 deletion syndrome 2022-01-03 criteria provided, single submitter clinical testing

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