rs876661113

chr7-5977587-C-Achr7-5977587-C-Gchr7-5977587-C-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1 PP3_Strong PP5_Very_Strong

The NM_000535.7(PMS2):c.2445+1G>T variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,395,778 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.000014 (1 hom.)
• Consequence: PMS2 NM_000535.7 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:16
• Conservation: PhyloP100: 7.90

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]

ACMG classification

Verdict is Pathogenic. Variant got 20 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 7-5977587-C-A is Pathogenic according to our data. Variant chr7-5977587-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 234604.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5977587-C-A is described in Lovd as [Pathogenic]. Variant chr7-5977587-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PMS2	NM_000535.7	c.2445+1G>T		splice_donor_variant		ENST00000265849.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PMS2	ENST00000265849.12	c.2445+1G>T		splice_donor_variant		1	NM_000535.7	P3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.0000143 AC: 20 AN: 1395778 Hom.: 1 Cov.: 29 AF XY: 0.0000129 AC XY: 9 AN XY: 695800

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000180

Gnomad4 OTH exome AF: 0.0000172

GnomAD4 genome Cov.: 30

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:16

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

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	GeneDx	Sep 20, 2023	Canonical splice site variant demonstrated to result in a null allele in a gene for which loss-of-function is a known mechanism of disease (van der Klift et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20205264, 25525159, 19132747, 27435373, 26110232, 23012243, 25512458, 24362816, 28702897, 26247049, 30787465, 33087929) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 05, 2020	The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. Found in at least one patient with expected phenotype for this gene, and not found in general population data. -

Lynch syndrome 4 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 22, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 23, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Sep 25, 2023	This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Aug 26, 2016

- -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The PMS2 c.2445+1G>T variant was identified in 3 of 1152 proband chromosomes (frequency: 0.003) from individuals or families with Lynch syndrome or colorectal cancer (Niessen 2009, Suerink 2015, ten Broeke 2015). The variant was also identified in dbSNP (ID: rs876661113) as "With Likely pathogenic, Pathogenic allele" and ClinVar (classified as pathogenic by Invitae, ARUP, Ambry Genetics and GeneDx). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The c.2445+1G>T variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. Further, RNA-based mutation scanning found this variant produced two aberrant splice products in cultured lymphocyte RNA (van der Klift 2015). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Aug 04, 2023

Variant summary: PMS2 c.2445+1G>T is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. At least one publication reports the variant to result in aberrant transcripts as assessed through minigene assays in HEK293 and HeLa cell lines and also, following analysis of patient RNA where retention of 85bp of flanking intronic sequence was observed (van der Klift_2015). The variant was absent in 194842 control chromosomes. c.2445+1G>T, has been reported in the literature in individuals affected with colorectal cancer (Niessen_2009, Vaughn_2010, ten Broeke_2015) or gynecological cancer (Delahunty_2022). The following publications have been ascertained in the context of this evaluation (PMID: 19132747, 26110232, 20205264, 25512458, 26247049, 35263119). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014; seven submitters classified the variant as pathogenic and one classified it as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Lynch syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 14, 2019

The c.2445+1G>T variant in PMS2 has been reported in at least 3 individuals suspected to have Lynch syndrome (Vaughn 2010, Niessen 2009, ten Broeke 2015). It was absent from large population studies and was classified as Pathogenic by several clinical labs (Variation ID 234604). This variant occurs within the canonical splice site (+/- 1,2) (within last intron) and is predicted to cause altered splicing leading to an abnormal or absent protein. Minigene assays and patient RNA studies demonstrate an impact on splicing (van der Klift 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PM2, PS4_Supporting, PVS1_Strong, PS3_Moderate. -

Lynch syndrome 4;C5436817:Mismatch repair cancer syndrome 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Apr 25, 2022

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 25, 2024

This sequence change affects a donor splice site in intron 14 of the PMS2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely disrupts the C-terminus of the 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. Disruption of this splice site has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 19132747, 20205264, 23012243, 25512458, 26110232). ClinVar contains an entry for this variant (Variation ID: 234604). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a new termination codon (PMID: 26247049; Invitae). However the mRNA is not expected to undergo nonsense-mediated decay. This variant disrupts a region of the PMS2 protein in which other variant(s) (p.Trp841Glyfs*10) have been determined to be pathogenic (PMID: 10037723, 16338176, 20533529, 26116798, 28218421). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 06, 2021

The c.2445+1G>T pathogenic mutation results from a G to T substitution one nucleotide after coding exon 14 of the PMS2 gene. This alteration has been reported in two HNPCC/Lynch syndrome patients: one with an MSI-H colorectal cancer diagnosed at 31 years of age and the other with a transverse colon cancer diagnosed at age 34 which demonstrated isolated absence of PMS2 on immunohistochemistry (IHC) (Niessen R et al. Genes Chromosomes Cancer. 2009 Apr;48(4):322-9; Vaughn C et al. Hum. Mutat. 2010 May;31(5):588-93). RNA studies for c.2445+1G>T demonstrated the presence of an aberrant transcript leading to premature protein truncation; however, levels of full-length/normal transcript were not assessed (van der Klift H et al. Mol. Genet. Genomic Med. 2015 Jul;3(4):327-45). This position is highly conserved in available vertebrate species. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein. As such, this alteration is classified as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.16
Cadd	Pathogenic	29
Dann	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Pathogenic	0.98	D
MutationTaster	Benign	1.0	D;D;D;D
GERP RS		5.8

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DL_spliceai		1.0		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs876661113; hg19: chr7-6017218;