ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.931C>T (p.Arg311Ter)

gnomAD frequency: 0.00001  dbSNP: rs386834039
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081807 SCV000113742 pathogenic not provided 2013-06-11 criteria provided, single submitter clinical testing
GeneDx RCV000081807 SCV000617417 pathogenic not provided 2018-12-24 criteria provided, single submitter clinical testing The R311X variant in the POMGNT1 gene has been reported previously in two unrelated individuals with muscle eye brain disease, both of whom harbored a second POMGNT1 variant (Biancheri et al., 2006; Saredi et al., 2012). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R311X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret R311X as a pathogenic variant.
Athena Diagnostics RCV000081807 SCV001145193 pathogenic not provided 2018-11-27 criteria provided, single submitter clinical testing The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and not found in general population data.
Invitae RCV001039421 SCV001202951 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2023-12-14 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg311*) in the POMGNT1 gene. It is expected to result in an absent or disrupted protein product. 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 premature translational stop signal has been observed in individuals with muscular dystrophy-dystroglycanopathy (PMID: 17030669, 22554691). ClinVar contains an entry for this variant (Variation ID: 56610). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003466920 SCV004206020 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 2022-09-06 criteria provided, single submitter clinical testing
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000050023 SCV000082432 probable-pathogenic Muscle eye brain disease no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Counsyl RCV000984204 SCV001132271 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2O 2015-04-02 no assertion criteria provided clinical testing
Counsyl RCV000984205 SCV001132272 likely pathogenic Retinitis pigmentosa 76 2015-04-02 no assertion criteria provided clinical testing
Counsyl RCV000050023 SCV001132471 likely pathogenic Muscle eye brain disease 2015-04-02 no assertion criteria provided clinical testing
Counsyl RCV000984300 SCV001132472 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2015-04-02 no assertion criteria provided clinical testing
Natera, Inc. RCV000050023 SCV001461195 pathogenic Muscle eye brain disease 2020-09-16 no assertion criteria provided clinical testing

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