ClinVar Miner

Submissions for variant NM_000252.3(MTM1):c.566A>G (p.Asn189Ser)

dbSNP: rs132630302
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000011802 SCV000193750 pathogenic Severe X-linked myotubular myopathy 2013-02-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000011802 SCV002178892 pathogenic Severe X-linked myotubular myopathy 2021-06-16 criteria provided, single submitter clinical testing This sequence change replaces asparagine with serine at codon 189 of the MTM1 protein (p.Asn189Ser). The asparagine residue is highly conserved and there is a small physicochemical difference between asparagine and serine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with myotubular myopathy (PMID: 8640223). In at least one individual the variant was observed to be de novo. This variant is also known as A620G, N207S. ClinVar contains an entry for this variant (Variation ID: 11053). 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 expected to disrupt MTM1 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV004700217 SCV005201746 likely pathogenic not provided 2024-01-28 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: 8640223, 10063835, Woo_2022[Article], 34011573)
OMIM RCV000011802 SCV000032035 pathogenic Severe X-linked myotubular myopathy 1996-06-01 no assertion criteria provided literature only

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