ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.1903G>A (p.Val635Ile)

gnomAD frequency: 0.00061  dbSNP: rs142299878
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000712836 SCV000226940 uncertain significance not provided 2018-04-18 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000175458 SCV000596541 uncertain significance not specified 2016-06-01 criteria provided, single submitter clinical testing
GeneDx RCV000712836 SCV000618095 uncertain significance not provided 2019-06-19 criteria provided, single submitter clinical testing Reported in a fetus with lissencephaly without an identified second POMT2 variant (Bouchet et al., 2007); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 17559086, 30564623)
Labcorp Genetics (formerly Invitae), Labcorp RCV000543953 SCV000649933 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 2022-09-13 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 635 of the POMT2 protein (p.Val635Ile). This variant is present in population databases (rs142299878, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with type II lissencephaly (PMID: 17559086). ClinVar contains an entry for this variant (Variation ID: 194965). 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) performed at Invitae indicates that this missense variant is not expected to disrupt 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.
Athena Diagnostics RCV000175458 SCV000843371 likely benign not specified 2021-03-31 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000763950 SCV000894897 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1; 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 2018-10-31 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000712836 SCV005409779 uncertain significance not provided 2023-06-13 criteria provided, single submitter clinical testing BP4

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