ClinVar Miner

Submissions for variant NM_182943.3(PLOD2):c.1855C>T (p.Arg619Cys)

gnomAD frequency: 0.00001  dbSNP: rs759871520
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001761263 SCV001998877 uncertain significance not provided 2020-08-11 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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
Neuberg Centre For Genomic Medicine, NCGM RCV001823307 SCV002072942 uncertain significance Bruck syndrome 2 criteria provided, single submitter clinical testing The missense variant p.R598C in PLOD2 (NM_000935.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.R598C variant is observed in 2/16,224 (0.0123%) alleles from individuals of African background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.R598C missense variant is predicted to be damaging by both SIFT and PolyPhen2. The arginine residue at codon 598 of PLOD2 is conserved in all mammalian species. The nucleotide c.1792 in PLOD2 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

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