ClinVar Miner

Submissions for variant NM_000245.4(MET):c.689C>T (p.Thr230Met)

gnomAD frequency: 0.00001  dbSNP: rs587780740
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002228448 SCV000166433 uncertain significance Renal cell carcinoma 2024-01-25 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 230 of the MET protein (p.Thr230Met). This variant is present in population databases (rs587780740, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with MET-related conditions. ClinVar contains an entry for this variant (Variation ID: 135975). 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 not expected to disrupt MET protein function with a negative predictive value of 80%. 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.
Illumina Laboratory Services, Illumina RCV000123131 SCV001324822 likely benign Papillary renal cell carcinoma type 1 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
GeneDx RCV001753507 SCV002006578 uncertain significance not provided 2019-06-28 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV002371957 SCV002667769 likely benign Hereditary cancer-predisposing syndrome 2022-12-16 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.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV002465528 SCV002760397 uncertain significance not specified 2023-08-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467092 SCV004192530 uncertain significance Autosomal recessive nonsyndromic hearing loss 97 2023-08-22 criteria provided, single submitter clinical testing

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