ClinVar Miner

Submissions for variant NM_015378.4(VPS13D):c.518G>A (p.Gly173Asp)

gnomAD frequency: 0.00031  dbSNP: rs185443968
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Cirak Lab, University Hospital Cologne RCV000855521 SCV000996651 uncertain significance Fetal akinesia deformation sequence 1; Arthrogryposis multiplex congenita 2019-06-28 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV001858520 SCV002277042 uncertain significance not provided 2022-10-27 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 173 of the VPS13D protein (p.Gly173Asp). This variant is present in population databases (rs185443968, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with multiple joint contractures (PMID: 31680123). ClinVar contains an entry for this variant (Variation ID: 692323). 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 VPS13D 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.
Breakthrough Genomics, Breakthrough Genomics RCV001858520 SCV005186468 uncertain significance not provided criteria provided, single submitter not provided
PreventionGenetics, part of Exact Sciences RCV004731046 SCV005338642 likely benign VPS13D-related disorder 2024-08-13 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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