ClinVar Miner

Submissions for variant NM_004370.6(COL12A1):c.5393C>T (p.Thr1798Met)

gnomAD frequency: 0.00010  dbSNP: rs370767331
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000534080 SCV000656167 uncertain significance Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1798 of the COL12A1 protein (p.Thr1798Met). This variant is present in population databases (rs370767331, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with COL12A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 475874). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV000534080 SCV000897310 uncertain significance Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2018-10-31 criteria provided, single submitter clinical testing
GeneDx RCV001591295 SCV001825152 uncertain significance not provided 2023-10-04 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function
Ambry Genetics RCV002525329 SCV003589892 uncertain significance Inborn genetic diseases 2022-10-03 criteria provided, single submitter clinical testing The c.5393C>T (p.T1798M) alteration is located in exon 31 (coding exon 30) of the COL12A1 gene. This alteration results from a C to T substitution at nucleotide position 5393, causing the threonine (T) at amino acid position 1798 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV001591295 SCV003832822 uncertain significance not provided 2020-08-13 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV001591295 SCV004223886 uncertain significance not provided 2022-12-22 criteria provided, single submitter clinical testing BP4

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