ClinVar Miner

Submissions for variant NM_014855.3(AP5Z1):c.2060C>G (p.Ser687Cys)

gnomAD frequency: 0.00019  dbSNP: rs201478168
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000225906 SCV000290018 uncertain significance Hereditary spastic paraplegia 48 2024-10-08 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 687 of the AP5Z1 protein (p.Ser687Cys). This variant is present in population databases (rs201478168, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with AP5Z1-related conditions. ClinVar contains an entry for this variant (Variation ID: 240938). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt AP5Z1 protein function with a negative predictive value of 80%. 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.
Athena Diagnostics RCV000518612 SCV000612376 uncertain significance not specified 2017-06-30 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV002261018 SCV002542271 uncertain significance not provided 2021-07-07 criteria provided, single submitter clinical testing
GeneDx RCV002261018 SCV002818989 uncertain significance not provided 2022-07-07 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV004816442 SCV005070431 uncertain significance Retinal dystrophy 2023-01-01 no assertion criteria provided clinical testing

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