ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1939G>A (p.Ala647Thr)

gnomAD frequency: 0.00001  dbSNP: rs119462987
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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) RCV000414180 SCV000336993 pathogenic not provided 2018-07-13 criteria provided, single submitter clinical testing
GeneDx RCV000414180 SCV000491141 pathogenic not provided 2024-05-30 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 18513969, 17869517, 22549409, 16717220, 24491487, 31589614, 30838351, 33963534, 19299310, 31066050, 17878207, 29419866, 34602496, 31031587, 34565739, 30454682, 35948506)
Labcorp Genetics (formerly Invitae), Labcorp RCV000694423 SCV000822869 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2023-12-06 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 669 of the POMT1 protein (p.Ala669Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with ongenital muscular dystrophy and limb girdle muscular dystrophy (PMID: 16717220, 17869517, 17878207, 20816175; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 3250). 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 POMT1 protein function. For these reasons, this variant has been classified as Pathogenic.
Athena Diagnostics RCV000414180 SCV000843357 likely pathogenic not provided 2017-09-14 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000414180 SCV004032889 likely pathogenic not provided 2023-07-01 criteria provided, single submitter clinical testing POMT1: PM3:Strong, PM2
Baylor Genetics RCV003460409 SCV004206053 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2024-01-23 criteria provided, single submitter clinical testing
OMIM RCV002286394 SCV000023564 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 2012-12-01 no assertion criteria provided literature only

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