Submissions for variant NM_022489.4(INF2):c.3563C>T (p.Ser1188Phe) (rs201715539)

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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000508357	SCV000604027	uncertain significance	not specified	2016-09-28	criteria provided, single submitter	clinical testing
GeneDx	RCV000508357	SCV000725143	likely benign	not specified	2017-12-01	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.
Illumina Clinical Services Laboratory,Illumina	RCV000370054	SCV000385308	likely benign	Focal segmental glomerulosclerosis	2016-06-14	criteria provided, single submitter	clinical testing
Invitae	RCV000649975	SCV000771812	uncertain significance	Focal segmental glomerulosclerosis 5; Charcot-Marie-Tooth disease, dominant intermediate E	2018-12-28	criteria provided, single submitter	clinical testing	This sequence change replaces serine with phenylalanine at codon 1188 of the INF2 protein (p.Ser1188Phe). The serine residue is moderately conserved and there is a large physicochemical difference between serine and phenylalanine. This variant is present in population databases (rs201715539, ExAC 0.06%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has not been reported in the literature in individuals with INF2-related disease. ClinVar contains an entry for this variant (Variation ID: 312711). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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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