Submissions for variant NM_006158.4(NEFL):c.1179G>C (p.Leu393Phe) (rs879253927)

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Total submissions: 3

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000235511	SCV000292835	uncertain significance	not specified	2015-04-28	criteria provided, single submitter	clinical testing	The L393F variant has not been published as pathogenic, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,100 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, the L393F variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic or a rare benign variant.
Invitae	RCV000640659	SCV000762254	uncertain significance	Charcot-Marie-Tooth disease type 2E	2018-12-26	criteria provided, single submitter	clinical testing	This sequence change replaces leucine with phenylalanine at codon 393 of the NEFL protein (p.Leu393Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with NEFL-related disease. ClinVar contains an entry for this variant (Variation ID: 245748). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Genesis Genome Database	RCV000857196	SCV000999778	uncertain significance	Charcot-Marie-Tooth disease	2019-08-14	no assertion criteria provided	research

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