rs63750451
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000535.7(PMS2):c.1882C>T(p.Arg628*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
PMS2
NM_000535.7 stop_gained
NM_000535.7 stop_gained
Scores
2
2
3
Clinical Significance
Conservation
PhyloP100: 1.60
Genes affected
PMS2 (HGNC:9122): (PMS1 homolog 2, mismatch repair system component) The protein encoded by this gene is a key component of the mismatch repair system that functions to correct DNA mismatches and small insertions and deletions that can occur during DNA replication and homologous recombination. This protein forms heterodimers with the gene product of the mutL homolog 1 (MLH1) gene to form the MutL-alpha heterodimer. The MutL-alpha heterodimer possesses an endonucleolytic activity that is activated following recognition of mismatches and insertion/deletion loops by the MutS-alpha and MutS-beta heterodimers, and is necessary for removal of the mismatched DNA. There is a DQHA(X)2E(X)4E motif found at the C-terminus of the protein encoded by this gene that forms part of the active site of the nuclease. Mutations in this gene have been associated with hereditary nonpolyposis colorectal cancer (HNPCC; also known as Lynch syndrome) and Turcot syndrome. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
Variant 7-5986883-G-A is Pathogenic according to our data. Variant chr7-5986883-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9242.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr7-5986883-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251434Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135908
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GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727236
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:16
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
not provided Pathogenic:5
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jun 07, 2023 | This variant causes the premature termination of PMS2 protein synthesis. In the published literature, this variant has been reported in individuals with colorectal cancer (PMIDs: 27589204 (2016), 27435373 (2016), 16472587 (2006)), breast cancer (PMID: 29345684 (2018)), ovarian/endometrial cancer (PMIDs: 29625052 (2018), 28888541 (2017)), and CMMRD (PMID: 27435373 (2016)). RNA analysis indicated the variant mRNA transcript is subjected to nonsense-mediated decay (PMID: 20186688 (2010)). The frequency of this variant in the general population, 0.000016 (4/251434 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 07, 2023 | Observed in individuals with PMS2-related cancers, including those with tumor studies consistent with pathogenic variants in this gene (Hendriks et al., 2006; van Puijenbroek et al., 2008; ten Broeke et al., 2015; Suerink et al., 2016; Sugano et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25980754, 20186688, 26110232, 30217226, 28888541, 29758216, 34697415, 25512458, 16472587, 18415027, 25691505, 27589204, 27435373, 28600700, 19283792, 25525159, 30787465, 29625052) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 03, 2021 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Lynch syndrome 4 Pathogenic:5
| Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2006 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Mar 16, 2016 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Sep 21, 2023 | This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 12, 2023 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Hereditary cancer-predisposing syndrome Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2022 | The p.R628* pathogenic mutation (also known as c.1882C>T), located in coding exon 11 of the PMS2 gene, results from a C to T substitution at nucleotide position 1882. This changes the amino acid from an arginine to a stop codon within coding exon 11. This mutation has been reported in several unrelated hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome patients and families; several with tumors demonstrating loss of PMS2 by immunohistochemistry (IHC) (Hendriks YM et al. Gastroenterology, 2006 Feb;130:312-22; van der Klift HM et al. Hum Mutat, 2010 May;31:578-87; Suerink M et al. Genet Med, 2016 Apr;18:405-9; Sugano K et al. Cancer Sci, 2016 Nov;107:1677-1686; Post CCB et al. J Natl Cancer Inst, 2021 Sep;113:1212-1220). This mutation has also been identified in two individuals with breast cancer undergoing multi-gene panel testing (Roberts ME et al. Genet. Med. 2018 10;20:1167-1174). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Oct 27, 2023 | This variant changes 1 nucleotide in exon 11 of the PMS2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in multiple individuals affected with colorectal or endometrial cancer that exhibited microsatellite instability and loss of PMS2 proteins by immunohistochemistry analyses (PMID: 16472587, 18415027, 27589204, 34253388, 36931573). This variant has also been reported in individuals affected with breast cancer (PMID: 16472587, 29345684). This variant has been identified in 4/251434 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PMS2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Aug 06, 2020 | - - |
Hereditary nonpolyposis colon cancer Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 24, 2019 | Variant summary: PMS2 c.1882C>T (p.Arg628X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. RT-PCR analysis on RNA derived from cultured lymphocytes of patients carrying the variant demonstrated nonsense-mediated RNA decay (van der Klift_2010, 2016). The variant allele was found at a frequency of 1.6e-05 in 251434 control chromosomes (gnomAD). c.1882C>T has been reported in the literature in multiple individuals affected with Lynch Syndrome (Hendriks_2006, Sugano_2016, van der Klift_2010, 2016). These data indicate that the variant is very likely to be associated with disease. Five ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Lynch syndrome Pathogenic:1
| Pathogenic, reviewed by expert panel | research | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Sep 05, 2013 | Coding sequence variation resulting in a stop codon - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | This sequence change creates a premature translational stop signal (p.Arg628*) in the PMS2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PMS2 are known to be pathogenic (PMID: 21376568, 24362816). This variant is present in population databases (rs63750451, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with constitutional mismatch repair deficiency syndrome and Lynch syndrome (PMID: 16472587, 19283792, 25512458, 26110232, 27435373, 27589204). ClinVar contains an entry for this variant (Variation ID: 9242). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at