ClinVar Miner

Submissions for variant NM_004370.6(COL12A1):c.5005G>C (p.Glu1669Gln)

gnomAD frequency: 0.00147  dbSNP: rs181511246
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000552072 SCV000656163 likely benign Ullrich congenital muscular dystrophy 2; Bethlem myopathy 2 2025-02-03 criteria provided, single submitter clinical testing
GeneDx RCV001591294 SCV001817393 likely benign not provided 2021-01-08 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001591294 SCV002497431 likely benign not provided 2022-06-01 criteria provided, single submitter clinical testing COL12A1: BP4, BS2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005239209 SCV005887583 likely benign not specified 2025-01-23 criteria provided, single submitter clinical testing Variant summary: COL12A1 c.5005G>C (p.Glu1669Gln) results in a conservative amino acid change located in the Fibronectin type-III domain (IPR003961) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0024 in 1461784 control chromosomes, predominantly at a frequency of 0.003 within the Non-Finnish European subpopulation in the gnomAD database, including 8 homozygotes. Frequency within Non-Finnish European subpopulation is similar to the estimated frequency for a pathogenic variant in COL12A1 causing Ullrich congenital muscular dystrophy 2 (0.003 vs 0.0035), suggesting the variant is likely benign. To our knowledge, no occurrence of c.5005G>C in individuals affected with early onset 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: 475871). Based on the evidence outlined above, the variant was classified as classified as likely benign.
PreventionGenetics, part of Exact Sciences RCV003905467 SCV004726696 likely benign COL12A1-related disorder 2021-05-04 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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