ClinVar Miner

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 pathogenic Charcot-Marie-Tooth disease type 2E 2020-08-20 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 been observed in individual(s) with autosomal dominant Charcot-Marie-Tooth disease (Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 245748). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NEFL protein function. For these reasons, this variant has been classified as Pathogenic.
Genesis Genome Database RCV000857196 SCV000999778 uncertain significance Charcot-Marie-Tooth disease 2019-08-14 no assertion criteria provided research

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