ClinVar Miner

Submissions for variant NM_004482.4(GALNT3):c.1626+1G>A

dbSNP: rs760830864
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV000008244 SCV002776931 pathogenic Tumoral calcinosis, hyperphosphatemic, familial, 1 2021-09-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003546453 SCV004270632 pathogenic not provided 2023-11-05 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 9 of the GALNT3 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with GALNT3-related conditions (PMID: 17311862). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 7801). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 17311862). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000008244 SCV000028451 pathogenic Tumoral calcinosis, hyperphosphatemic, familial, 1 2007-05-01 no assertion criteria provided literature only

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