ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.1691C>T (p.Thr564Met)

gnomAD frequency: 0.00023  dbSNP: rs142445941
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000518453 SCV000614754 uncertain significance not specified 2017-03-13 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000727260 SCV000707048 uncertain significance not provided 2017-03-21 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000695518 SCV000824024 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2; Autosomal recessive limb-girdle muscular dystrophy type 2N 2022-10-03 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 564 of the POMT2 protein (p.Thr564Met). This variant is present in population databases (rs142445941, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with POMT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 448116). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on POMT2 protein function. 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.
CeGaT Center for Human Genetics Tuebingen RCV000727260 SCV001149282 uncertain significance not provided 2016-05-01 criteria provided, single submitter clinical testing
GeneDx RCV000727260 SCV001791724 uncertain significance not provided 2019-04-11 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV000727260 SCV003809715 uncertain significance not provided 2022-05-27 criteria provided, single submitter clinical testing

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