ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.1531C>G (p.His511Asp)

gnomAD frequency: 0.00004  dbSNP: rs762634619
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000559298 SCV000641808 uncertain significance Vici syndrome 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with aspartic acid, which is acidic and polar, at codon 511 of the EPG5 protein (p.His511Asp). This variant is present in population databases (rs762634619, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with EPG5-related conditions. ClinVar contains an entry for this variant (Variation ID: 466237). 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 EPG5 protein function. 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.
GeneDx RCV001569770 SCV001793913 uncertain significance not provided 2020-06-25 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function Observed on 0.1725% (61/35368 alleles) from individuals of Latino background in the ExAC dataset, which is greater than expected for this disorder (Lek et al., 2016) Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002526143 SCV003705311 likely benign Inborn genetic diseases 2022-06-29 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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