ClinVar Miner

Submissions for variant NM_080680.3(COL11A2):c.3173C>T (p.Pro1058Leu)

gnomAD frequency: 0.00003  dbSNP: rs562253142
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000503631 SCV000594187 uncertain significance not specified 2017-03-16 criteria provided, single submitter clinical testing
GeneDx RCV000657862 SCV000779622 uncertain significance not provided 2023-04-28 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 has a deleterious effect on protein structure/function
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000657862 SCV000885210 uncertain significance not provided 2018-03-19 criteria provided, single submitter clinical testing The COL11A2 c.3173C>T; p.Pro1058Leu variant (rs562253142, ClinVar variant ID 434809), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.004% (identified on 10 out of 276,252 chromosomes). The proline at position 1058 is highly conserved, considering 11 species, and computational analyses of the effects of the p.Pro1058Leu variant on protein structure and function predict a deleterious effect (SIFT: damaging, PolyPhen-2: probably damaging). Based on the available information, the clinical significance of the p.Pro1058Leu variant cannot be determined with certainty.
Invitae RCV000657862 SCV002317442 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000657862 SCV003831158 uncertain significance not provided 2021-10-13 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003932823 SCV004750429 uncertain significance COL11A2-related condition 2023-12-26 criteria provided, single submitter clinical testing The COL11A2 c.3173C>T variant is predicted to result in the amino acid substitution p.Pro1058Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.025% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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