ClinVar Miner

Submissions for variant NM_000535.7(PMS2):c.1638_1639del (p.Ser547fs) (rs863224498)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000198235 SCV000253846 pathogenic Hereditary nonpolyposis colon cancer 2020-01-09 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser547Argfs*14) in the PMS2 gene. It is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with PMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 216075). Loss-of-function variants in PMS2 are known to be pathogenic (PMID: 21376568, 24362816). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000479164 SCV000570067 pathogenic not provided 2016-04-21 criteria provided, single submitter clinical testing This deletion of 2 nucleotides in PMS2 is denoted c.1638_1639delTT at the cDNA level and p.Ser547ArgfsX14 (S547RfsX14) at the protein level. The normal sequence, with the bases that are deleted in braces, is CTTT[TT]CAGA. The deletion causes a frameshift which changes a Serine to an Arginine at codon 547, and creates a premature stop codon at position 14 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. We consider this variant to be pathogenic.

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