ClinVar Miner

Submissions for variant NM_002335.4(LRP5):c.3122C>T (p.Thr1041Met)

gnomAD frequency: 0.00001  dbSNP: rs1311935185
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002004821 SCV002231995 pathogenic not provided 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1041 of the LRP5 protein (p.Thr1041Met). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individuals with clinical features of autosomal dominant exudative retinopathy (PMID: 30452590; Invitae). ClinVar contains an entry for this variant (Variation ID: 1450334). 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 LRP5 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002276951 SCV002564889 uncertain significance Osteogenesis imperfecta 2018-10-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005050476 SCV005684848 likely pathogenic 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 2024-04-29 criteria provided, single submitter clinical testing

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