ClinVar Miner

Submissions for variant NM_001330078.2(NRXN1):c.3103A>G (p.Thr1035Ala)

gnomAD frequency: 0.00001  dbSNP: rs753262049
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726048 SCV000341502 uncertain significance not provided 2016-06-02 criteria provided, single submitter clinical testing
GeneDx RCV000726048 SCV000618944 uncertain significance not provided 2017-07-11 criteria provided, single submitter clinical testing The T1075A variant has not been published as a pathogenic variant, nor has it been reported as abenign variant to our knowledge. It is not observed at a significant frequency in large populationcohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Thisvariant is a non-conservative amino acid substitution that occurs at a position that is not conserved.In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to theprotein structure/function. Therefore, based on the currently available information, it is unclearwhether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000817074 SCV000957614 uncertain significance Pitt-Hopkins-like syndrome 2 2023-12-21 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1075 of the NRXN1 protein (p.Thr1075Ala). This variant is present in population databases (rs753262049, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 287664). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

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