7-5991999-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000535.7(PMS2):ā€‹c.962T>Cā€‹(p.Val321Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000939 in 1,597,510 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.000020 ( 0 hom., cov: 31)
Exomes š‘“: 0.0000083 ( 0 hom. )

Consequence

PMS2
NM_000535.7 missense

Scores

2
13
4

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts P:1U:12

Conservation

PhyloP100: 8.92
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PMS2NM_000535.7 linkc.962T>C p.Val321Ala missense_variant 9/15 ENST00000265849.12 NP_000526.2 P54278-1Q7Z3Q2B4DGM0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PMS2ENST00000265849.12 linkc.962T>C p.Val321Ala missense_variant 9/151 NM_000535.7 ENSP00000265849.7 P54278-1

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152186
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000318
AC:
8
AN:
251268
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135840
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000435
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000830
AC:
12
AN:
1445206
Hom.:
0
Cov.:
27
AF XY:
0.00000278
AC XY:
2
AN XY:
720132
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000253
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.12e-7
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152304
Hom.:
0
Cov.:
31
AF XY:
0.0000403
AC XY:
3
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000189
ExAC
AF:
0.0000247
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:12
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Lynch syndrome 4 Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsOct 20, 2023- -
Uncertain significance, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Apr 04, 2023This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk. -
Uncertain significance, criteria provided, single submitterclinical testingCounsylFeb 03, 2017- -
not provided Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJun 20, 2022In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified in an individual with colorectal cancer whose tumor demonstrated absence of MLH1 and PMS2 on immunohistochemistry as well as individuals with a personal or family history of breast or ovarian cancer (Jiang 2019, Kwong 2020, Shao 2020); This variant is associated with the following publications: (PMID: 32661327, 31742824, 32068069, 11574484, 30521064, 31269945) -
Uncertain significance, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJun 12, 2017- -
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 05, 2023The p.V321A variant (also known as c.962T>C), located in coding exon 9 of the PMS2 gene, results from a T to C substitution at nucleotide position 962. The valine at codon 321 is replaced by alanine, an amino acid with similar properties. This alteration was identified in a 61 year old male with colorectal cancer demonstrating loss of MLH1 and PMS2 proteins by IHC whose family history did not meet Amsterdam criteria II (Jiang W et al. Int J Cancer, 2019 05;144:2161-2168). This alteration was also identified in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Kwong A et al. J Mol Diagn, 2020 Apr;22:544-554; Shao D et al. Cancer Sci, 2020 Feb;111:647-657). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthOct 05, 2023This missense variant replaces valine with alanine at codon 321 of the PMS2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals affected with colorectal cancer, one whose tumor displayed PMS2 protein loss via immunohistochemistry analysis and the other whose tumor displayed PMS2 and MLH1 protein loss with no MLH1 methylation detected (PMID: 30521064). The variant has also been observe in individuals with either personal or family history of breast and/or ovarian cancer (PMID: 31742824, 32068069). This variant has been identified in 9/282634 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Ovarian cancer Pathogenic:1
Likely pathogenic, flagged submissionclinical testingLaboratory of Molecular Epidemiology of Birth Defects, West China Second University Hospital, Sichuan UniversityJan 01, 2022- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpFeb 26, 2021Variant summary: PMS2 c.962T>C (p.Val321Ala) results in a non-conservative amino acid change located in the DNA mismatch repair protein family, N-terminal domain and DNA mismatch repair protein, S5 domain 2-like domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 251268 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.962T>C has been reported in the literature in individuals affected with colorectal cancer, familial adenomatous polyposis, breast and/or ovarian cancer (Jiang_2019, Kim_2019, Shao_2019, Kwong_2020). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. One co-occurrence with another pathogenic variant has been reported (APC c.3927_3931del, p.Glu1309AspfsTer4, Kim_2019), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Lynch syndrome 1 Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingDing PR Lab, Sun Yat-sen University Cancer Center-- -
Lynch syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthOct 23, 2023This missense variant replaces valine with alanine at codon 321 of the PMS2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals affected with colorectal cancer, one whose tumor displayed PMS2 protein loss via immunohistochemistry analysis and the other whose tumor displayed PMS2 and MLH1 protein loss with no MLH1 methylation detected (PMID: 30521064). The variant has also been observe in individuals with either personal or family history of breast and/or ovarian cancer (PMID: 31742824, 32068069). This variant has been identified in 9/282634 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Hereditary nonpolyposis colorectal neoplasms Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 30, 2025This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 321 of the PMS2 protein (p.Val321Ala). This variant is present in population databases (rs186448384, gnomAD 0.04%). This missense change has been observed in individual(s) with PMS2-related conditions (PMID: 30521064, 34897210, 35449176, 36243179). ClinVar contains an entry for this variant (Variation ID: 219846). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is not expected to disrupt PMS2 function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Lynch syndrome 4;C5436817:Mismatch repair cancer syndrome 4 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsMar 21, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Uncertain
0.025
T
BayesDel_noAF
Uncertain
0.12
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.44
T;.;.;.;.
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.63
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.93
D;D;.;D;.
M_CAP
Benign
0.049
D
MetaRNN
Uncertain
0.66
D;D;D;D;D
MetaSVM
Uncertain
0.23
D
MutationAssessor
Benign
1.7
L;.;.;.;.
PrimateAI
Uncertain
0.64
T
PROVEAN
Uncertain
-3.3
D;D;.;.;.
REVEL
Pathogenic
0.72
Sift
Uncertain
0.0030
D;D;.;.;.
Sift4G
Uncertain
0.0030
D;D;.;.;.
Polyphen
1.0
D;D;.;.;D
Vest4
0.76
MVP
0.90
MPC
0.29
ClinPred
0.73
D
GERP RS
5.4
Varity_R
0.73
gMVP
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs186448384; hg19: chr7-6031630; COSMIC: COSV105851239; API