ClinVar Miner

Submissions for variant NM_001365902.3(NFIX):c.1408G>A (p.Ala470Thr)

gnomAD frequency: 0.00011  dbSNP: rs372257657
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000827369 SCV000969012 likely benign not provided 2018-05-17 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001858421 SCV002294974 uncertain significance Marshall-Smith syndrome; Malan overgrowth syndrome 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 478 of the NFIX protein (p.Ala478Thr). This variant is present in population databases (rs372257657, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NFIX-related conditions. ClinVar contains an entry for this variant (Variation ID: 668469). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Not Available"; Align-GVGD: "Not Available". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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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