ClinVar Miner

Submissions for variant NM_004329.3(BMPR1A):c.1571T>C (p.Met524Thr)

gnomAD frequency: 0.00001  dbSNP: rs1843703476
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001059132 SCV001223742 uncertain significance Juvenile polyposis syndrome 2023-06-05 criteria provided, single submitter clinical testing 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. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on BMPR1A protein function. ClinVar contains an entry for this variant (Variation ID: 854154). This variant has not been reported in the literature in individuals affected with BMPR1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 524 of the BMPR1A protein (p.Met524Thr).
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV003238294 SCV002009871 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV003307891 SCV004001518 uncertain significance Hereditary cancer-predisposing syndrome 2023-06-12 criteria provided, single submitter clinical testing The p.M524T variant (also known as c.1571T>C), located in coding exon 11 of the BMPR1A gene, results from a T to C substitution at nucleotide position 1571. The methionine at codon 524 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV003307891 SCV004360105 uncertain significance Hereditary cancer-predisposing syndrome 2022-01-24 criteria provided, single submitter clinical testing This missense variant replaces methionine with threonine at codon 524 of the BMPR1A protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
All of Us Research Program, National Institutes of Health RCV001059132 SCV004838525 uncertain significance Juvenile polyposis syndrome 2024-01-11 criteria provided, single submitter clinical testing This missense variant replaces methionine with threonine at codon 524 of the BMPR1A protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Baylor Genetics RCV004570236 SCV005058171 uncertain significance Polyposis syndrome, hereditary mixed, 2 2024-02-08 criteria provided, single submitter clinical testing
GeneDx RCV003238294 SCV005391625 uncertain significance not provided 2024-03-17 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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