ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1792C>T (p.Arg598Ter)

gnomAD frequency: 0.00001  dbSNP: rs761848742
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000487062 SCV000567636 pathogenic not provided 2015-08-04 criteria provided, single submitter clinical testing The R620X nonsense variant in the POMT1 gene has been reported previously in a fetus with type IIlissencephaly who harbored a second POMT1 variant on the other chromosome (Bouchet et al., 2007). Thisvariant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. R620X was not observed in approximately 6,500 individuals ofEuropean and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not acommon benign variant in these populations. Therefore, R620X is considered a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV002525809 SCV003256215 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2024-01-15 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg620*) in the POMT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in POMT1 are known to be pathogenic (PMID: 12369018, 15637732, 16575835). This variant is present in population databases (rs761848742, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with POMT1-related conditions (PMID: 17559086, 22323514, 31311558). ClinVar contains an entry for this variant (Variation ID: 419671). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003464000 SCV004206049 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2024-01-19 criteria provided, single submitter clinical testing

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