ClinVar Miner

Submissions for variant NM_000302.4(PLOD1):c.1667A>G (p.Tyr556Cys)

gnomAD frequency: 0.00016  dbSNP: rs146360295
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522723 SCV000620483 uncertain significance not provided 2024-10-21 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function
Labcorp Genetics (formerly Invitae), Labcorp RCV000634755 SCV000756098 uncertain significance Ehlers-Danlos syndrome, kyphoscoliotic type 1 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 556 of the PLOD1 protein (p.Tyr556Cys). This variant is present in population databases (rs146360295, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with PLOD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 451743). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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.
CeGaT Center for Human Genetics Tuebingen RCV000522723 SCV001247281 uncertain significance not provided 2019-08-01 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000522723 SCV001712971 uncertain significance not provided 2019-11-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002404348 SCV002708423 uncertain significance Familial thoracic aortic aneurysm and aortic dissection 2023-12-12 criteria provided, single submitter clinical testing The c.1667A>G (p.Y556C) alteration is located in exon 16 (coding exon 16) of the PLOD1 gene. This alteration results from a A to G substitution at nucleotide position 1667, causing the tyrosine (Y) at amino acid position 556 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Fulgent Genetics, Fulgent Genetics RCV000634755 SCV002791631 uncertain significance Ehlers-Danlos syndrome, kyphoscoliotic type 1 2022-04-05 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004525959 SCV005040571 uncertain significance not specified 2024-03-31 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000522723 SCV005186464 uncertain significance not provided criteria provided, single submitter not provided

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