Submissions for variant NM_004370.6(COL12A1):c.4463C>G (p.Thr1488Ser)

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV002771342	SCV003029629	uncertain significance	Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2	2022-09-13	criteria provided, single submitter	clinical testing	In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 not expected to disrupt COL12A1 protein function. This variant has not been reported in the literature in individuals affected with COL12A1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 1488 of the COL12A1 protein (p.Thr1488Ser).
GeneDx	RCV003232671	SCV003929652	uncertain significance	not provided	2022-12-02	criteria provided, single submitter	clinical testing	Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); At the protein level, in silico analysis supports that this missense variant does not alter protein structure/function; At the mRNA level, in silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.