ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.236-1G>T

gnomAD frequency: 0.00001  dbSNP: rs1057516477
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409804 SCV000485746 likely pathogenic Muscle eye brain disease 2016-02-09 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001377077 SCV001574310 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2024-01-20 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 3 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). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 370425). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Baylor Genetics RCV003463789 SCV004205992 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 2023-03-28 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005018701 SCV005648545 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3; Retinitis pigmentosa 76 2024-06-01 criteria provided, single submitter clinical testing

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