ClinVar Miner

Submissions for variant NM_000393.5(COL5A2):c.3309G>A (p.Pro1103=)

dbSNP: rs878853978
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002229654 SCV000284814 pathogenic Ehlers-Danlos syndrome, classic type, 1 2023-07-31 criteria provided, single submitter clinical testing 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 is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 237775). This variant has been observed in individual(s) with COL5A2-related disease (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). This sequence change affects codon 1103 of the COL5A2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the COL5A2 protein. This variant also falls at the last nucleotide of exon 46, which is part of the consensus splice site for this exon.
Revvity Omics, Revvity RCV001782722 SCV002023317 likely pathogenic Ehlers-Danlos syndrome, classic type, 2 2020-05-28 criteria provided, single submitter clinical testing
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV001782722 SCV002072914 uncertain significance Ehlers-Danlos syndrome, classic type, 2 criteria provided, single submitter clinical testing The synonymous variant p.P1103= in COL5A2 (NM_000393.5) has been submitted to ClinVar as a Pathogenic de novo variant but no details are available for independent assesment. It has not been reported in affected individuals in literature. The p.P1103= variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. In silico splice algorithms do not predict a damaging effect. For these reasons, this variant has been classified as Uncertain significance.

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