ClinVar Miner

Submissions for variant NM_002335.4(LRP5):c.1613G>A (p.Arg538Gln)

gnomAD frequency: 0.00003  dbSNP: rs138692892
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001339367 SCV001533107 uncertain significance not provided 2024-05-28 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 538 of the LRP5 protein (p.Arg538Gln). This variant is present in population databases (rs138692892, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LRP5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1036364). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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 RCV001339367 SCV002038967 uncertain significance not provided 2021-06-16 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533)
CeGaT Center for Human Genetics Tuebingen RCV001339367 SCV004137093 uncertain significance not provided 2022-11-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005050341 SCV005684354 uncertain significance Bone mineral density quantitative trait locus 1; Exudative vitreoretinopathy 4; Worth disease; Autosomal dominant osteopetrosis 1; Osteoporosis with pseudoglioma; Polycystic liver disease 4 with or without kidney cysts 2024-04-19 criteria provided, single submitter clinical testing

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