ClinVar Miner

Submissions for variant NM_002427.4(MMP13):c.619T>G (p.Trp207Gly)

gnomAD frequency: 0.00005  dbSNP: rs140059558
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000303456 SCV000341124 likely pathogenic not provided 2018-08-02 criteria provided, single submitter clinical testing
Baylor Genetics RCV000162347 SCV001524343 pathogenic Metaphyseal chondrodysplasia, Spahr type 2020-06-10 criteria provided, single submitter clinical testing This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Invitae RCV000303456 SCV001586089 pathogenic not provided 2024-01-03 criteria provided, single submitter clinical testing This sequence change replaces tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 207 of the MMP13 protein (p.Trp207Gly). This variant is present in population databases (rs140059558, gnomAD 0.01%). This missense change has been observed in individuals with autosomal recessive metaphyseal dysplasia, Spahr type (PMID: 24648384, 27576021; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 183687). 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 expected to disrupt MMP13 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000303456 SCV001872883 likely pathogenic not provided 2021-03-23 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24648384, 27576021, 31130284, 13915518)
Revvity Omics, Revvity RCV000303456 SCV002023492 likely pathogenic not provided 2021-11-11 criteria provided, single submitter clinical testing
OMIM RCV000162347 SCV000212650 pathogenic Metaphyseal chondrodysplasia, Spahr type 2014-05-01 no assertion criteria provided literature only
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000162347 SCV000854742 pathogenic Metaphyseal chondrodysplasia, Spahr type 2018-06-06 no assertion criteria provided clinical testing

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