ClinVar Miner

Submissions for variant NM_004369.3(COL6A3):c.6156G>C (p.Lys2052Asn) (rs398124125)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723513 SCV000112866 uncertain significance not provided 2013-11-19 criteria provided, single submitter clinical testing
GeneDx RCV000723513 SCV000621515 uncertain significance not provided 2017-10-12 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the COL6A3 gene. The c.6156 G>C variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.6156 G>C variant is not observed in large population cohorts (Lek et al., 2016). Several in-silico splice prediction models predict that c.6156 G>C weakens or destroys the natural donor site for intron 15 which may lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. If the c.6156 G>C variant does not affect splicing, it will result in the K2052N missense change. The K2052N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species; and in silico analysis predicts this variant is probably damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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