ClinVar Miner

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

gnomAD frequency: 0.00003  dbSNP: rs149682171
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175455 SCV000226937 pathogenic not provided 2015-04-17 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000648152 SCV000769966 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 653 of the POMT1 protein (p.Pro653Leu). This variant is present in population databases (rs149682171, gnomAD 0.01%). This missense change has been observed in individual(s) with POMT1-related conditions (PMID: 24491487, 31311558, 34925456). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 194962). Invitae Evidence 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 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 POMT1 protein function. 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.
Revvity Omics, Revvity RCV000175455 SCV002019492 pathogenic not provided 2023-03-08 criteria provided, single submitter clinical testing
Baylor Genetics RCV004567380 SCV005052411 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2024-03-21 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005049457 SCV005674912 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 2024-04-22 criteria provided, single submitter clinical testing

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