ClinVar Miner

Submissions for variant NM_019109.5(ALG1):c.1187+1G>A

gnomAD frequency: 0.00002  dbSNP: rs374928784
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081984 SCV000113919 pathogenic not provided 2013-10-08 criteria provided, single submitter clinical testing
GeneDx RCV000081984 SCV000617788 pathogenic not provided 2016-04-20 criteria provided, single submitter clinical testing The c.1187+1 G>A splice site variant in the ALG1 gene has been previously reported in association with congenital disorders of glycosylation (Jones et al., 2013; Ng et al., 2016). This pathogenic variant destroys the canonical splice donor site in intron 11, and is expected to cause abnormal gene splicing. Therefore, we interpret c.1187+1 G>A to be a pathogenic variant.
Fulgent Genetics, Fulgent Genetics RCV002505001 SCV002807980 pathogenic ALG1-congenital disorder of glycosylation 2021-12-29 criteria provided, single submitter clinical testing
Invitae RCV002505001 SCV003514022 pathogenic ALG1-congenital disorder of glycosylation 2023-10-09 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 11 of the ALG1 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 ALG1 are known to be pathogenic (PMID: 20679665, 23806237). This variant is present in population databases (rs374928784, gnomAD 0.003%). Disruption of this splice site has been observed in individuals with clinical features of congenital disorder of glycosylation type 1 (PMID: 23806237, 32064623). ClinVar contains an entry for this variant (Variation ID: 95934). 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.
University of Washington Center for Mendelian Genomics, University of Washington RCV000851244 SCV000993496 likely pathogenic Congenital disorder of glycosylation 2017-05-25 no assertion criteria provided research

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