rs886039646

Positions:

• chr7-5973466-CA-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_Moderate PP5_Very_Strong

The NM_000535.7(PMS2):​c.2521delT​(p.Trp841fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: 𝑓 0.000038 (0 hom., cov: 10)
• Consequence: PMS2 NM_000535.7 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 9.32

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]

PMS2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0263 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PP5: Variant 7-5973466-CA-C is Pathogenic according to our data. Variant chr7-5973466-CA-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 265586.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMS2	NM_000535.7	c.2521delT	p.Trp841fs	frameshift_variant	15/15	ENST00000265849.12	NP_000526.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PMS2	ENST00000265849.12	c.2521delT	p.Trp841fs	frameshift_variant	15/15	1	NM_000535.7	ENSP00000265849.7

Frequencies

GnomAD3 genomes AF: 0.0000383 AC: 3 AN: 78260 Hom.: 0 Cov.: 10

Gnomad AFR AF: 0.0000981

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000259

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 9

GnomAD4 genome AF: 0.0000383 AC: 3 AN: 78346 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 36188

Gnomad4 AFR AF: 0.0000978

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000259

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 03, 2024	Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 22 amino acids are lost and replaced with 9 incorrect amino acids; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26691941, 28218421, 30764633, 30787465, 16338176, 20533529, 10037723, 31992580, Fukui2011[Chapter], 31997046, 31447099, 33948563, 26116798) -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 16, 2024	The PMS2 c.2521del; p.Trp841GlyfsTer10 variant (rs886039646; ClinVar ID: 265586) is reported in the literature in heterozygous individuals with a diagnosis or suspicion of Lynch syndrome (Brand 2020, Wang 2020) and is also reported in the homozygous or compound heterozygous state in individuals with constitutional mismatch repair-deficiency (Bodo 2015, Maletzki 2017, Pavlova 2024). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. This variant results in a premature termination codon in the last exon of the PMS2 gene. While this may not lead to nonsense-mediated decay, it is expected to create a truncated protein lacking the final 22 amino acids. Based on available information, this variant is considered to be likely pathogenic. References: Bodo S et al. Diagnosis of Constitutional Mismatch Repair-Deficiency Syndrome Based on Microsatellite Instability and Lymphocyte Tolerance to Methylating Agents. Gastroenterology. 2015 Oct;149(4):1017-29.e3. PMID: 26116798. Brand RE et al. Detection of DNA mismatch repair deficient crypts in random colonoscopic biopsies identifies Lynch syndrome patients. Fam Cancer. 2020 Apr;19(2):169-175. PMID: 31997046. Maletzki C et al. Frameshift mutational target gene analysis identifies similarities and differences in constitutional mismatch repair-deficiency and Lynch syndrome. Mol Carcinog. 2017 Jul;56(7):1753-1764. PMID: 28218421. Palova H et al. Precision immuno-oncology approach for four malignant tumors in siblings with constitutional mismatch repair deficiency syndrome. NPJ Precis Oncol. 2024 May 21;8(1):110. PMID: 38773265. Wang Q et al. Characterisation of heterozygous PMS2 variants in French patients with Lynch syndrome. J Med Genet. 2020 Jul;57(7):487-499. PMID: 31992580. -
Likely pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The PMS2 p.Trp841Glyfs*10 variant was not identified in the literature however it was identified in dbSNP (ID: rs886039646) as “With Pathogenic allele”, ClinVar (classified with conflicting interpretations of pathogenicity; submitters: pathogenic by Ambry Genetics, likely pathogenic by GeneDx and Invitae and uncertain significance by Integrated Genetics/Laboratory Corporation of America), and Clinvitae (3x). The variant was not identified in COGR, Cosmic, Insight Colon Cancer Gene Variant Database, Zhejiang University Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors Database. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.2521del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 841 and leads to a premature stop codon 10 codons downstream. This alteration is then predicted to result in a truncated or absent protein however the variant is located at the C-term of the protein and it is unclear if this truncation would lead to nonsense mediated decay or loss of function. Notable there are no truncating variants 3’ of this variant listed as pathogenic in ClinVar. However studies have shown that the C-term of PMS2 is important for binding to MLH1 which is integral to PMS2 function (Kosinski 2010, Guerrette 1999). Loss of function variants of the PMS2 gene are an established mechanism of disease in Lynch syndrome and is the type of variant expected to cause the disorder. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 10, 2023

This variant disrupts the MLH1 interaction domain of the PMS2 protein, which has been shown to be critical for PMS2-MLH1 dimerization (PMID: 10037723), and therefore mismatch repair activity (PMID: 16338176, 20533529). While functional studies have not been performed to directly test the effect of this variant on PMS2 protein function, this suggests that disruption of this region of the protein is causative of disease. For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Trp841Glyfs*10) in the PMS2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 22 amino acid(s) of the PMS2 protein. The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This premature translational stop signal has been observed in individuals with clinical features of constitutional mismatch repair deficiency syndrome and/or clinical features of Lynch syndrome (PMID: 28218421, 30764633; Invitae). ClinVar contains an entry for this variant (Variation ID: 265586). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects PMS2 function (PMID: 26116798). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 03, 2022

The c.2521delT pathogenic mutation, located in coding exon 15 of the PMS2 gene, results from a deletion of one nucleotide at nucleotide position 2521, causing a translational frameshift with a predicted alternate stop codon (p.W841Gfs*10). This alteration occurs at the 3' terminus of thePMS2 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 22 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function (Ambry internal data). This variant has been identified in probands whose Lynch syndrome-associated tumors demonstrated high microsatellite instability and/or loss of PMS2 expression by immunohistochemistry (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Mismatch repair cancer syndrome 1 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 17, 2019

Variant summary: PMS2 c.2521delT (p.Trp841GlyfsX10) results in a premature termination codon in the last exon of the PMS2 mRNA, predicted to cause a truncation and disrupt the last 22 amino acids (Trp841-Asn862) of the PMS2 protein. The variant was absent in 177052 control chromosomes (in gnomAD). However, the variant c.2523G>A (p.Trp841X) has been observed in 64/10632 African alleles in gnomAD, including 3 homozygotes, suggesting loss of the far end of C-terminal of PMS2 protein (the last 22 amino acids Trp841-Asn862) is likely tolerable, although the technology utilized for this dataset does not rule out pseudogene interference and thus this data might not be relied upon. It was shown in an in vitro study that the C-terminal (amino acids 675-850) region of PMS2 is critical for PMS2-MLH1 dimerization , as the interaction was lost for the tested protein fragment truncated at amino acid 825 (Guerrette 1999), suggesting the region between amino acids 825-850 is critical for PMS2-MLH1 interaction. However, from these data the impact of truncation at amino acid 841 cannot be determined for the MLH1 interaction. The variant, c.2521delT, has been reported in the literature in two individuals affected with constitutional mismatch repair deficiency (CMMRD) syndrome. In one case it was found in homozygosity in a 4 years old patient diagnosed with high-grade glioma (Bodo 2015, Maletzki 2017), in the other case it was found in co-occurrence with the pathogenic PMS2 variant (c.2T>A (p.Met1Lys); Machackova 2016). The homozygous patient was from a consanguineous family, where three relatives were affected with Lynch syndrome- or CMMRD-associated cancers on the maternal side (they were diagnosed at the the age 5, 9 and 15 years). In functional studies performed on lymphoblastoid cell lines (LCLs) derived from the patient carrying the variant in homozygosity, MSI (microsatellite instability) and tolerance to methylating agents could be demonstrated (while these changes couldn't be shown in LCLs from MMR-proficient controls, including Lynch syndrome patients; Bodo 2015). In another study, authors demonstrated MSI in the tumor obtained from the homozygous patient (Maletzki 2017). These results suggest that the variant is probably associated with the disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Three classified as likely pathogenic/pathogenic while one classified as VUS. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Lynch syndrome 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 10, 2024

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs886039646; hg19: chr7-6013097;