ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp) (rs398124244)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000177268 SCV000229112 likely pathogenic not provided 2013-11-27 criteria provided, single submitter clinical testing
Invitae RCV001376971 SCV001574181 likely pathogenic Limb-girdle muscular dystrophy-dystroglycanopathy, type C1; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1; Walker-Warburg congenital muscular dystrophy 2020-10-30 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with aspartic acid at codon 44 of the POMT1 protein (p.Glu44Asp). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and aspartic acid. This variant is present in population databases (rs398124244, ExAC 0.003%). This variant has been observed in individual(s) with congenital muscular dystrophy (PMID: 27159402). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 95456). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant disrupts the p.Glu44 amino acid residue in POMT1. Other variant(s) that disrupt this residue have been observed in individuals with POMT1-related conditions (PMID: 27193224), which suggests that this may be a clinically significant amino acid residue. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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