ClinVar Miner

Submissions for variant NM_001278074.1(COL5A1):c.3983C>G (p.Pro1328Arg) (rs140797509)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000198960 SCV000249826 likely benign not specified 2018-01-02 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001086728 SCV000283490 likely benign Ehlers-Danlos syndrome, classic type 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000387669 SCV000478565 uncertain significance Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000622144 SCV000738601 uncertain significance Cardiovascular phenotype 2016-03-10 criteria provided, single submitter clinical testing Insufficient or conflicting evidence
Center for Human Genetics, Inc,Center for Human Genetics, Inc RCV000680508 SCV000807892 uncertain significance Connective tissue disease 2018-06-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000755967 SCV000883656 uncertain significance not provided 2018-03-04 criteria provided, single submitter clinical testing The COL5A1 c.3983C>G; p.Pro1328Arg variant (rs140797509; ClinVar variant ID 212969), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.04% (identified on 76 out of 179,884 chromosomes) and an Ashkenazi Jewish population frequency of 0.07% (identified on 61 out of 8,548 chromosomes). The proline at position 1328 is highly conserved, considering 12 species, and computational analyses of the effects of the p.Pro1328Arg variant on protein structure and function make conflicting predictions (SIFT: tolerated, PolyPhen-2: probably damaging). Based on the available information, the clinical significance of the p.Pro1328Arg variant cannot be determined with certainty.
Illumina Clinical Services Laboratory,Illumina RCV001086728 SCV001328145 likely benign Ehlers-Danlos syndrome, classic type 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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