ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1760G>A (p.Ser587Asn) (rs762100304)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000569664 SCV000663427 likely benign Hereditary cancer-predisposing syndrome 2018-08-24 criteria provided, single submitter clinical testing Other strong data supporting benign classification;In silico models in agreement (benign)
Invitae RCV000629864 SCV000750820 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2019-09-27 criteria provided, single submitter clinical testing This sequence change replaces serine with asparagine at codon 587 of the PMS2 protein (p.Ser587Asn). The serine residue is weakly conserved and there is a small physicochemical difference between serine and asparagine. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been observed in an individual with stomach adenocarcinoma (PMID: 26689913). ClinVar contains an entry for this variant (Variation ID: 480298). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Counsyl RCV000662639 SCV000785325 uncertain significance Hereditary nonpolyposis colorectal cancer type 4 2017-07-06 criteria provided, single submitter clinical testing
Color RCV000569664 SCV000903116 likely benign Hereditary cancer-predisposing syndrome 2018-07-27 criteria provided, single submitter clinical testing

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