ClinVar Miner

Submissions for variant NM_000089.3(COL1A2):c.2425C>T (p.Pro809Ser) (rs145355907)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497839 SCV000589466 uncertain significance not provided 2017-12-21 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the COL1A2 gene. The P809S variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is observed in 27/66740 (0.04%) alleles from individuals of European ancestry in the Exome Aggregation Consortium (ExAC) dataset (Lek et al., 2016; Exome Variant Server). The P809S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, this variant lacks observation in a significant number of affected individuals, segregation data, and functional evidence, which would further clarify its pathogenicity.
Invitae RCV001085263 SCV000627314 likely benign Ehlers-Danlos syndrome, classic type; Osteogenesis imperfecta type I 2019-12-31 criteria provided, single submitter clinical testing
Center for Human Genetics, Inc,Center for Human Genetics, Inc RCV000680488 SCV000807866 uncertain significance Connective tissue disease 2018-06-01 criteria provided, single submitter clinical testing
Undiagnosed Diseases Network,NIH RCV000791269 SCV000930555 uncertain significance Predisposition to dissection 2019-03-22 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000497839 SCV001155149 uncertain significance not provided 2016-11-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001164726 SCV001326875 benign EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 2 2018-01-12 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 RCV001164727 SCV001326876 likely benign Osteogenesis imperfecta 2018-01-12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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