ClinVar Miner

Submissions for variant NM_182943.3(PLOD2):c.475A>T (p.Ile159Phe)

gnomAD frequency: 0.00008  dbSNP: rs768122346
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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 RCV001919368 SCV002189944 uncertain significance not provided 2021-09-17 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with phenylalanine at codon 159 of the PLOD2 protein (p.Ile159Phe). The isoleucine residue is moderately conserved and there is a small physicochemical difference between isoleucine and phenylalanine. This variant is present in population databases (rs768122346, ExAC 0.05%). This variant has not been reported in the literature in individuals affected with PLOD2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002276935 SCV002564981 uncertain significance Osteogenesis imperfecta 2020-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV004044144 SCV005007709 uncertain significance Inborn genetic diseases 2023-12-22 criteria provided, single submitter clinical testing The c.475A>T (p.I159F) alteration is located in exon 4 (coding exon 4) of the PLOD2 gene. This alteration results from a A to T substitution at nucleotide position 475, causing the isoleucine (I) at amino acid position 159 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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