ClinVar Miner

Submissions for variant NM_001844.5(COL2A1):c.342+5G>A

dbSNP: rs2136629166
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001769044 SCV002002425 uncertain significance not provided 2020-07-13 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); Intronic +5 splice site variant in a gene for which loss-of-function is a known mechanism of disease, and both splice predictors and evolutionary conservation support a deleterious effect, although in the absence of functional evidence the actual effect of this sequence change is unknown.
Labcorp Genetics (formerly Invitae), Labcorp RCV001769044 SCV003210845 pathogenic not provided 2022-07-09 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the COL2A1 gene. It does not directly change the encoded amino acid sequence of the COL2A1 protein. It affects a nucleotide within the consensus splice site. For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1313093). This variant has been observed in individual(s) with clinical features of Stickler syndrome (Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency).

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