ClinVar Miner

Submissions for variant NM_001365902.3(NFIX):c.373A>G (p.Lys125Glu)

dbSNP: rs2145192745
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV001782525 SCV002020121 likely pathogenic not provided 2020-12-17 criteria provided, single submitter clinical testing
GeneDx RCV001782525 SCV003195076 pathogenic not provided 2023-01-17 criteria provided, single submitter clinical testing Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.K125E due to the use of an alternate transcript; This variant is associated with the following publications: (PMID: 29897170, 26193383)
Invitae RCV002544267 SCV003443179 pathogenic Marshall-Smith syndrome; Malan overgrowth syndrome 2022-08-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Lys133 amino acid residue in NFIX. Other variant(s) that disrupt this residue have been observed in individuals with NFIX-related conditions (PMID: 29142766), which suggests that this may be a clinically significant amino acid residue. 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: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1324805). This variant is also known as c.373A>G, p.Lys125Glu. This missense change has been observed in individual(s) with NFIX-related conditions (PMID: 26193383; Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 133 of the NFIX protein (p.Lys133Glu).

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