ClinVar Miner

Submissions for variant NM_001037333.3(CYFIP2):c.1684C>T (p.Arg562Trp)

gnomAD frequency: 0.00001  dbSNP: rs1663188420
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001249779 SCV001423814 likely pathogenic CYFIP2-related neurodevelopmental disorders 2019-10-14 criteria provided, single submitter clinical testing The CYFIP2 c.1759C>T (p.Arg587Trp) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is not found in the Genome Aggregation Database despite good sequence coverage, so the variant is presumed to be rare. The Arg587 residue is located in the FragX_IP interacting domain (Zweier et al. 2019). Based on the de novo nature of the variant and application of ACMG criteria, the p.Arg587Trp is classified as likely pathogenic for CYFIP2-related neurodevelopmental disorders.
Labcorp Genetics (formerly Invitae), Labcorp RCV001879764 SCV002225533 uncertain significance not provided 2021-05-21 criteria provided, single submitter clinical testing 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. 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"). This variant has not been reported in the literature in individuals with CYFIP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 973327). This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with tryptophan at codon 562 of the CYFIP2 protein (p.Arg562Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan.

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