ClinVar Miner

Submissions for variant NM_017739.3(POMGNT1):c.636C>T (p.Phe212=) (rs190057175)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000255207 SCV000322258 pathogenic not provided 2017-08-04 criteria provided, single submitter clinical testing The c.636 C>T variant in the POMGNT1 gene has been reported previously in homozygous and compound heterozygous patients with POMGNT1-related disorders (Bouchet et al., 2007; Oliveira et al., 2008; Valencia et al., 2013). Functional studies indicate that c.636 C>T leads to skipping of exon 7, which results in a frameshift and reduced levels of POMGNT1 protein as compared to controls (Oliveira et al., 2008). The c.636 C>T variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating is not a common benign variant in these populations.
Invitae RCV000695969 SCV000824510 pathogenic Limb-girdle muscular dystrophy-dystroglycanopathy, type C3; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3 2018-11-08 criteria provided, single submitter clinical testing This sequence change affects codon 212 of the POMGNT1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the POMGNT1 protein. This variant is present in population databases (rs190057175, ExAC 0.003%). This variant has been reported as homozygous or compound heterozygous in many individuals affected with lissencephaly or congenital muscular dystrophy (PMID: 17559086, 28424332, 18330676, 22323514, 23326386). ClinVar contains an entry for this variant (Variation ID: 265399). Experimental studies have shown that this silent change causes exon 7 skipping, leading to a frameshift and introduction of a premature termination codon (PMID: 17559086, 28424332, 18330676). For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000984296 SCV001132467 likely pathogenic Muscle eye brain disease 2014-01-23 no assertion criteria provided clinical testing
Counsyl RCV000984297 SCV001132468 likely pathogenic Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3 2014-01-23 no assertion criteria provided clinical testing
Counsyl RCV000984298 SCV001132469 likely pathogenic Limb-girdle muscular dystrophy-dystroglycanopathy, type C3 2014-01-23 no assertion criteria provided clinical testing
Counsyl RCV000984299 SCV001132470 likely pathogenic Retinitis pigmentosa 76 2014-01-23 no assertion criteria provided clinical testing

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