ClinVar Miner

Submissions for variant NM_152490.5(B3GALNT2):c.1368+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1479230229
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001901679 SCV002174722 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2023-07-17 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with B3GALNT2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 11 of the B3GALNT2 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. ClinVar contains an entry for this variant (Variation ID: 1404510). 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. This variant disrupts a region of the B3GALNT2 protein in which other variant(s) (p.Pro474del) have been determined to be pathogenic (PMID: 26663670, 33290285). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001901679 SCV003829701 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2021-09-09 criteria provided, single submitter clinical testing

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