ClinVar Miner

Submissions for variant NM_001844.5(COL2A1):c.803C>T (p.Pro268Leu) (rs142770543)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000296689 SCV000379052 benign Type II Collagenopathies 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000351659 SCV000379053 uncertain significance Stickler syndrome type 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000481919 SCV000564898 uncertain significance not specified 2017-09-15 criteria provided, single submitter clinical testing The P268L variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P268L variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The P268L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. However, this substitution occurs at a position that is not conserved across species, and where leucine is wild-type in multiple species. Finally, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function.
Fulgent Genetics,Fulgent Genetics RCV000763850 SCV000894780 uncertain significance Achondrogenesis type II; Avascular necrosis of the head of femur; Epiphyseal dysplasia, multiple, with myopia and conductive deafness; Coxa plana; Kniest dysplasia; Osteoarthritis with mild chondrodysplasia; Spondyloperipheral dysplasia-short ulna syndrome; Stickler syndrome type 1; Platyspondylic dysplasia, Torrance type; Spondylometaphyseal dysplasia; Spondyloepiphyseal dysplasia congenita; Czech dysplasia, metatarsal type; Stickler syndrome, type I, nonsyndromic ocular; Spondyloepiphyseal dysplasia, stanescu type 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000976095 SCV001123990 likely benign not provided 2019-12-31 criteria provided, single submitter clinical testing

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