ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.713G>A (p.Ser238Asn)

gnomAD frequency: 0.00001  dbSNP: rs1060503111
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000470673 SCV000551928 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2023-10-14 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 238 of the PMS2 protein (p.Ser238Asn). This variant is present in population databases (no rsID available, gnomAD 0.004%). This missense change has been observed in individual(s) with breast cancer (PMID: 35449176). ClinVar contains an entry for this variant (Variation ID: 411017). 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 PMS2 protein function. 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.
Ambry Genetics RCV000569996 SCV000664904 uncertain significance Hereditary cancer-predisposing syndrome 2020-10-21 criteria provided, single submitter clinical testing The p.S238N variant (also known as c.713G>A), located in coding exon 7 of the PMS2 gene, results from a G to A substitution at nucleotide position 713. The serine at codon 238 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated 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 RCV000569996 SCV000910191 uncertain significance Hereditary cancer-predisposing syndrome 2023-08-23 criteria provided, single submitter clinical testing This missense variant replaces serine with asparagine at codon 238 of the PMS2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with PMS2-related disorders in the literature. This variant has been identified in 1/226824 chromosomes 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.
Mendelics RCV000987844 SCV001137316 likely benign Lynch syndrome 4 2019-05-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV000987844 SCV004207832 uncertain significance Lynch syndrome 4 2023-05-25 criteria provided, single submitter clinical testing

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