ClinVar Miner

Submissions for variant NM_001844.5(COL2A1):c.1679G>C (p.Arg560Pro)

gnomAD frequency: 0.00001  dbSNP: rs1186241291
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001568822 SCV001792759 uncertain significance not provided 2019-10-30 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001568822 SCV002981686 uncertain significance not provided 2022-10-17 criteria provided, single submitter clinical testing 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. ClinVar contains an entry for this variant (Variation ID: 1202957). This variant has not been reported in the literature in individuals affected with COL2A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 560 of the COL2A1 protein (p.Arg560Pro).
GenomeConnect - Brain Gene Registry RCV003325999 SCV004032180 not provided Achondrogenesis type II; Kniest dysplasia; Stickler syndrome type 1; Platyspondylic dysplasia, Torrance type; Spondyloepiphyseal dysplasia congenita; Spondyloepiphyseal dysplasia with metatarsal shortening; Hypochondrogenesis; Spondyloepimetaphyseal dysplasia, Strudwick type no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 02-21-2019 by Lab GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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