ClinVar Miner

Submissions for variant NM_004370.6(COL12A1):c.5839C>A (p.Pro1947Thr)

gnomAD frequency: 0.00023  dbSNP: rs191233787
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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 RCV000536812 SCV000656173 likely benign Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2025-01-25 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000536812 SCV000895789 uncertain significance Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2021-08-16 criteria provided, single submitter clinical testing
GeneDx RCV001551411 SCV001771917 uncertain significance not provided 2021-11-01 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; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 475878; Landrum et al., 2016)
Revvity Omics, Revvity RCV001551411 SCV003831224 likely benign not provided 2023-03-03 criteria provided, single submitter clinical testing
New York Genome Center RCV000536812 SCV004176112 uncertain significance Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2023-06-16 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005239213 SCV005883426 likely benign not specified 2024-12-16 criteria provided, single submitter clinical testing Variant summary: COL12A1 c.5839C>A (p.Pro1947Thr) results in a non-conservative amino acid change located in the Fibronectin type III repeat domain (IPR003961) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00019 in 1614188 control chromosomes in the gnomAD database (v4.1 dataset), including 1 homozygote. To our knowledge, no occurrence of c.5839C>A in individuals affected with Ullrich congenital muscular dystrophy 2 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 475878). Based on the evidence outlined above, the variant was classified as likely benign.

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