ClinVar Miner

Submissions for variant NM_017739.3(POMGNT1):c.355G>A (p.Val119Met) (rs148498470)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485011 SCV000573489 uncertain significance not provided 2017-03-01 criteria provided, single submitter clinical testing The V119M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V119M variant is observed in 13/66378 (0.02%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variant in a nearby residue (L120R) has been reported in the Human Gene Mutation Database in association with autosomal recessive retinitis pigmentosa (Stenson et al., 2014).
Fulgent Genetics,Fulgent Genetics RCV000763936 SCV000894881 uncertain significance Muscle eye brain disease; Limb-girdle muscular dystrophy-dystroglycanopathy, type C3; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3; Retinitis pigmentosa 76 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000817043 SCV000957579 uncertain significance Limb-girdle muscular dystrophy-dystroglycanopathy, type C3; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B3 2018-12-28 criteria provided, single submitter clinical testing This sequence change replaces valine with methionine at codon 119 of the POMGNT1 protein (p.Val119Met). The valine residue is highly conserved and there is a small physicochemical difference between valine and methionine. This variant is present in population databases (rs148498470, ExAC 0.02%). This variant has not been reported in the literature in individuals with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 423754). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

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