ClinVar Miner

Submissions for variant NM_207122.2(EXT2):c.536+1G>A

dbSNP: rs1954091762
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001584830 SCV001813745 pathogenic not provided 2023-06-12 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 10713884, 30730578)
Labcorp Genetics (formerly Invitae), Labcorp RCV002569114 SCV003440365 pathogenic Exostoses, multiple, type 2 2022-04-01 criteria provided, single submitter clinical testing Disruption of this splice site has been observed in individual(s) with hereditary multiple exostoses (PMID: 10713884). ClinVar contains an entry for this variant (Variation ID: 1211965). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. This sequence change affects a donor splice site in intron 2 of the EXT2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EXT2 are known to be pathogenic (PMID: 10679937, 19810120). This variant is not present in population databases (gnomAD no frequency).

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