ClinVar Miner

Submissions for variant NM_002335.4(LRP5):c.164C>T (p.Ser55Phe)

gnomAD frequency: 0.00011  dbSNP: rs148462220
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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 RCV001344923 SCV001539009 uncertain significance not provided 2024-10-25 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 55 of the LRP5 protein (p.Ser55Phe). This variant is present in population databases (rs148462220, gnomAD 0.03%). 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: 1041160). 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) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on LRP5 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.
Fulgent Genetics, Fulgent Genetics RCV002486402 SCV002781453 uncertain significance Bone mineral density quantitative trait locus 1; Exudative vitreoretinopathy 4; Exudative vitreoretinopathy 1; Worth disease; Autosomal dominant osteopetrosis 1; Osteoporosis with pseudoglioma; Osteoporosis; Polycystic liver disease 4 with or without kidney cysts 2021-12-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV004036439 SCV004899338 uncertain significance Inborn genetic diseases 2021-09-16 criteria provided, single submitter clinical testing The c.164C>T (p.S55F) alteration is located in exon 2 (coding exon 2) of the LRP5 gene. This alteration results from a C to T substitution at nucleotide position 164, causing the serine (S) at amino acid position 55 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV001344923 SCV005392132 uncertain significance not provided 2024-04-11 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001344923 SCV005879398 uncertain significance not provided 2024-08-14 criteria provided, single submitter clinical testing The LRP5 c.164C>T; p.Ser55Phe variant (rs148462220), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 1041160). This variant is observed in the general population with an overall allele frequency of 0.01% (39/281868 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.559). Due to limited information, the clinical significance of this variant is uncertain at this time.

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