ClinVar Miner

Submissions for variant NM_017739.3(POMGNT1):c.643C>T (p.Arg215Ter) (rs386834034)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute RCV000408610 SCV000484423 pathogenic Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3 2015-08-21 criteria provided, single submitter clinical testing This homozygous variant is predicted to create a premature stop at position 215, NP_001230695.1(POMGNT1): p.(Arg215*). In-silico models predict this to be deleterious. This variant has not previously been reported in disease databases. It is present at a very low frequency in teh ExAC database (3/120592 alleles, all heterozygous), which would be consistent with a carrier rate for a rare condition. The parents were confirmed to be carriers.
GeneDx RCV000578838 SCV000680688 pathogenic not provided 2017-06-14 criteria provided, single submitter clinical testing The R215X variant in the POMGNT1 gene has been reported previously in the homozygous state in an individual with severe intellectual disability, hypotonia, pachygyria, polymicrogyria, and seizures (Stark et al., 2016). It has also been reported in the compound heterozygous state, along with a second nonsense variant, in an individual with muscle eye brain disease (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 R215X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret R215X as a pathogenic variant.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000050017 SCV000082426 probable-pathogenic Muscle eye brain disease no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Counsyl RCV000050017 SCV001132463 likely pathogenic Muscle eye brain disease 2014-01-02 no assertion criteria provided clinical testing
Counsyl RCV000408610 SCV001132464 likely pathogenic Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3 2014-01-02 no assertion criteria provided clinical testing
Counsyl RCV000984294 SCV001132465 likely pathogenic Limb-girdle muscular dystrophy-dystroglycanopathy, type C3 2014-01-02 no assertion criteria provided clinical testing
Counsyl RCV000984295 SCV001132466 likely pathogenic Retinitis pigmentosa 76 2014-01-02 no assertion criteria provided clinical testing

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