ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1539+1G>T

dbSNP: rs138642840
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049996 SCV000793042 pathogenic Muscle eye brain disease 2017-07-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002513695 SCV003522660 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2021-12-06 criteria provided, single submitter clinical testing 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: 56583). This variant is also known as IVS17+1G>T. Disruption of this splice site has been observed in individuals with muscle-eye-brain disease (PMID: 11709191). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 17 of the POMGNT1 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 POMGNT1 are known to be pathogenic (PMID: 19299310, 20816175, 21447391, 26908613, 27391550).
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049996 SCV000082405 pathogenic Muscle eye brain disease no assertion criteria provided not provided Converted during submission to Pathogenic.

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