ClinVar Miner

Submissions for variant NM_018344.6(SLC29A3):c.300+1G>A

gnomAD frequency: 0.00001  dbSNP: rs587780463
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118377 SCV000152777 pathogenic H syndrome 2014-02-03 criteria provided, single submitter clinical testing
3billion RCV000118377 SCV002058999 pathogenic H syndrome 2022-01-03 criteria provided, single submitter clinical testing Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_VS).The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000130339).It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000064, PM2_M). Each parent is heterozygous for the variant (PM3_P, 3billion dataset). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Invitae RCV000118377 SCV002234641 pathogenic H syndrome 2023-05-16 criteria provided, single submitter clinical testing This variant is present in population databases (rs587780463, gnomAD 0.03%). This sequence change affects a donor splice site in intron 2 of the SLC29A3 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 SLC29A3 are known to be pathogenic (PMID: 19336477, 20595384, 23406517, 25963354). For these reasons, this variant has been classified as Pathogenic. 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: 130339). Disruption of this splice site has been observed in individuals with SLC29A3-related conditions (PMID: 20140240, 27215564).
OMIM RCV000118377 SCV000045227 pathogenic H syndrome 2010-02-05 no assertion criteria provided literature only

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