ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1150G>A (p.Gly384Ser) (rs146234177)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000658067 SCV000339026 uncertain significance not provided 2018-02-27 criteria provided, single submitter clinical testing
GeneDx RCV000658067 SCV000779838 uncertain significance not provided 2018-05-23 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the POMT1 gene. The G406S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G406S variant is observed in 9/34342 (0.03%) alleles from individuals of Latino background in large population cohorts (Lek et al., 2016). The G406S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000694581 SCV000823032 uncertain significance Limb-girdle muscular dystrophy-dystroglycanopathy, type C1; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1; Walker-Warburg congenital muscular dystrophy 2018-11-16 criteria provided, single submitter clinical testing This sequence change replaces glycine with serine at codon 406 of the POMT1 protein (p.Gly406Ser). The glycine residue is highly conserved and there is a small physicochemical difference between glycine and serine. This variant is present in population databases (rs146234177, ExAC 0.02%). This variant has not been reported in the literature in individuals with POMT1-related disease. ClinVar contains an entry for this variant (Variation ID: 285835). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics,Fulgent Genetics RCV000764806 SCV000895951 uncertain significance Limb-girdle muscular dystrophy-dystroglycanopathy, type C1; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 1; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 2018-10-31 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000658067 SCV001145177 uncertain significance not provided 2018-11-16 criteria provided, single submitter clinical testing

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