ClinVar Miner

Submissions for variant NM_001130144.3(LTBP3):c.1620C>T (p.Pro540=)

gnomAD frequency: 0.00003  dbSNP: rs200693646
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000615364 SCV000727200 likely benign not specified 2018-01-30 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV002404679 SCV002708035 likely benign Inborn genetic diseases 2022-07-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp RCV003754881 SCV004399910 uncertain significance Brachyolmia-amelogenesis imperfecta syndrome 2023-12-30 criteria provided, single submitter clinical testing This sequence change affects codon 540 of the LTBP3 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the LTBP3 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs200693646, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with LTBP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 515186). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.
Breakthrough Genomics, Breakthrough Genomics RCV004704127 SCV005212989 likely benign not provided criteria provided, single submitter not provided
PreventionGenetics, part of Exact Sciences RCV003962817 SCV004776388 likely benign LTBP3-related disorder 2024-02-05 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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