ClinVar Miner

Submissions for variant NM_000393.5(COL5A2):c.3316C>T (p.Arg1106Trp) (rs146789395)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000196302 SCV000250019 uncertain significance not specified 2017-01-04 criteria provided, single submitter clinical testing The R1106W variant in the COL5A2 gene has not been reported as a disease-causing variant or as a benign polymorphism to our knowledge. The NHLBI Exome Sequencing Project and the 1000 Genomes Project reports R1106W was observed in 0.4% to 0.9% of alleles from individuals of African American ancestry, indicating it may be a rare benign variant in this population. In addition, no missense variants in nearby residues have been reported in association with EDS, classic type indicating this region of the protein may be tolerant of change. Nevertheless, R1106W results in a non-conservative amino acid substitution of a positively-charged Arginine with a neutral Tryptophan at a position that is well conserved across species. Furthermore, in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000333952 SCV000425626 likely benign Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000475732 SCV000558989 benign Ehlers-Danlos syndrome, classic type 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000617926 SCV000738696 uncertain significance Cardiovascular phenotype 2018-01-22 criteria provided, single submitter clinical testing Insufficient or conflicting evidence
Center for Human Genetics, Inc,Center for Human Genetics, Inc RCV000659484 SCV000781299 uncertain significance Connective tissue disease 2016-11-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001141923 SCV001302310 benign Ehlers-Danlos syndrome classic 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.

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