ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1892C>T (p.Pro631Leu) (rs149682171)

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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 RCV000175455 SCV000226937 pathogenic not provided 2015-04-17 criteria provided, single submitter clinical testing
Invitae RCV000648152 SCV000769966 likely pathogenic Limb-girdle muscular dystrophy-dystroglycanopathy, type C1; Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1; Walker-Warburg congenital muscular dystrophy 2017-08-17 criteria provided, single submitter clinical testing This sequence change replaces proline with leucine at codon 653 of the POMT1 protein (p.Pro653Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. This variant is present in population databases (rs149682171, ExAC 0.01%). This variant has been reported in combination with another pathogenic POMT1 variant to segregate with early onset muscular dystrophy and intellectual disability with minimal structural brain anomalies and no ocular abnormalities in a single family and an unrelated individual with motor and speech delays and microcephaly (PMID: 24491487). ClinVar contains an entry for this variant (Variation ID: 194962). 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. 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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