--- title: "PMS2 R628X (c.1882C>T, rs63750451) | Dante Labs" description: "ClinVar classifies PMS2 R628X as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/pms2/variants/r628x" --- 1. [Genes](https://dantelabs.com/genes) 2. [PMS2](https://dantelabs.com/genes/pms2) 3. PMS2 R628X Variant # PMS2 R628X NM_000535.7(PMS2):c.1882C>T (p.Arg628Ter) Also known as - p.Arg628Ter - p.R628\* - rs63750451 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 5 September 2013 * Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bf Facts last changed 16 October 2026 ## Summary R628X is a nonsense variant in PMS2: it creates an early stop signal, so the protein the gene encodes is predicted to be cut short. ClinVar classifies it as pathogenic for Lynch Syndrome (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | ---------------- | | [Lynch Syndrome](https://dantelabs.com/conditions/lynch-syndrome) [ClinVar VCV000009242 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/9242/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 5 September 2013 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## Where it lies in PMS2 R628X lies in exon 11 of the 15 in PMS2's MANE Select transcript, NM_000535.7. [PMS2 variants in exon 11 →](https://dantelabs.com/genes/pms2/variants?exon=11) [PMS2's gene diagram →](https://dantelabs.com/genes/pms2#gene-structure) ## Molecular details | Gene | [PMS2](https://dantelabs.com/genes/pms2) | | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000535.7 MANE Select | | Coding DNA change (HGVS c.) | c.1882C>T | | Protein change (HGVS p.) | p.Arg628Ter p.R628\* | | Predicted consequence | Nonsense (stop gained) [stop_gained (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001587) | | Predicted impact | High | | Position (GRCh38) | chr7:5986883 G>A | | Position (GRCh37) | chr7:6026514 G>A | | dbSNP ID | [rs63750451 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs63750451) | | ClinVar Variation ID | [VCV000009242 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/9242/) | | ClinVar Allele ID | 24281 | | ClinGen Allele Registry ID | [CA010399 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA010399) | | ClinVar name | NM_000535.7(PMS2):c.1882C>T (p.Arg628Ter) | ## PMS2 R628X in other databases - [ClinVar VCV000009242 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/9242/) - [dbSNP rs63750451 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs63750451) - [ClinGen Allele Registry CA010399 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA010399) - [gnomAD 7-5986883-G-A (opens in a new tab)](https://gnomad.broadinstitute.org/variant/7-5986883-G-A?dataset=gnomad_r4) - [Ensembl rs63750451 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs63750451) ## Reports that look at this variant (1) These Genome Test condition reports include R628X among the variants they look at. | Report | Conditions | Inheritance | | ----------------------------------------------------------------- | -------------- | ------------------ | | [Lynch Syndrome](https://dantelabs.com/conditions/lynch-syndrome) | Lynch Syndrome | Autosomal dominant | ### A harder region to sequence R628X lies in a part of the genome that short-read sequencing reads less reliably, such as a repeated or highly similar stretch of DNA. Variants in regions like this can be missed or miscalled, and are usually confirmed with another method. - Segmental duplications Regions from the Genome in a Bottle Consortium's difficult-region tracks. ## Other variants in PMS2 - [c.1A>G Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-1a-g) - [c.24-12_107delinsAAAT Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-24-12to107delinsaaat) - [c.163+2T>C Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-163plus2t-c) - [c.164-2A>G Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-164-2a-g) - [c.164-518_803+252delinsCG Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-164-518to803plus252delinscg) - [c.251-2A>G Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-251-2a-g) - [c.538-478_705+456del Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-538-478to705plus456del) - [c.705+1G>T Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-705plus1g-t) - [c.989-2A>G Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-989-2a-g) - [c.989-296_1144+706del Pathogenic 3 stars out of 4](https://dantelabs.com/genes/pms2/variants/c-989-296to1144plus706del) [All PMS2 variants](https://dantelabs.com/genes/pms2/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026. ## Cite this page APA > Dante Labs. (16 October 2026). PMS2 R628X (c.1882C>T, rs63750451) (Version 2026.10.16-c6eea6bf). Retrieved 17 October 2026, from https\://dantelabs.com/genes/pms2/variants/r628x Vancouver > Dante Labs. PMS2 R628X (c.1882C>T, rs63750451) \[Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 \[cited 17 October 2026]. Available from: https\://dantelabs.com/genes/pms2/variants/r628x Download citation [RIS](https://dantelabs.com/genes/pms2/variants/r628x/cite.ris) [BibTeX](https://dantelabs.com/genes/pms2/variants/r628x/cite.bib) [CSL-JSON](https://dantelabs.com/genes/pms2/variants/r628x/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)