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COVID-19 research

Gene: PMS2

Green List (high evidence)

PMS2 (PMS1 homolog 2, mismatch repair system component)
EnsemblGeneIds (GRCh38): ENSG00000122512
EnsemblGeneIds (GRCh37): ENSG00000122512
OMIM: 600259, Gene2Phenotype
PMS2 is in 34 panels

3 reviews

Sophie Hambleton (Newcastle University)

I don't know

Seems rarely to present as immunodeficiency
Created: 29 Jun 2018, 3:03 p.m.

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with Mismatch repair cancer syndrome 276300 and Colorectal cancer, hereditary nonpolyposis, type 4 614337 in OMIM and as confirmed Gen2Phen gene for both of these phenotypes. At least 13 variants reported Mismatch repair cancer syndrome 276300 and 6 in Colorectal cancer, hereditary nonpolyposis, type 4 614337.
Created: 9 May 2018, 12:37 p.m.
Comment on mode of inheritance: Monoallelic for Colorectal cancer, hereditary nonpolyposis, type 4 614337 and biallelic for Mismatch repair cancer syndrome 276300
Created: 9 May 2018, 12:26 p.m.
Comment on phenotypes: Variants in PMS2 also associated with Colorectal cancer, hereditary nonpolyposis, type 4 614337
Created: 9 May 2018, 12:22 p.m.

Louise Daugherty (Genomics England Curator)

I don't know

Keep Amber until more info on gene and disease association regarding immunological phenotype, external expert review denotes it rarely presents as immunodeficiency
Created: 4 Jul 2018, 5:52 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): PMS2 .PanelApp HGNC gene symbol check: PMS2 . IUIS Disease: PMS2 Deficiency . IUIS Inheritance: AR .T cells: Poor activation, proliferation, motility, .B cells: Low B cells, switched and non-switched , .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: DNA Repair Defects other than those listed in Table 1
Created: 2 Jul 2018, 10:35 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: PMS2, PanelApp HGNC gene symbol check: PMS2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / DNA-breakage disorder / Post-Meiotic Segregation 2 (PMS2) deficiency; Predominantly antibody disorders / Class switch recombination defects (CSR) / HIGM syndromes / CSR defects and Hyper IgM (HIGM) syndromes
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: PMS2, GRID_Gene_Symbol: PMS2, GRID_Transcript_ENS_Community submitted: ENST00000265849, GRID_Transcript_RefSeq: NM_000535.5, GRID_Transcript_ENS_used_on_Production: ENST00000265849
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors
  • Post-Meiotic Segregation 2 (PMS2) deficiency
  • Mismatch repair cancer syndrome 276300
  • Combined immunodeficiencies with associated or syndromic features
  • CSR defects and Hyper IgM (HIGM) syndromes
  • Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors
OMIM
600259
Clinvar variants
Variants in PMS2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to PMS2. Added phenotypes Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Post-Meiotic Segregation 2 (PMS2) deficiency; Mismatch repair cancer syndrome 276300; Combined immunodeficiencies with associated or syndromic features; CSR defects and Hyper IgM (HIGM) syndromes; Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors for gene: PMS2 Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 2

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: PMS2 was added gene: PMS2 was added to Viral susceptibility. Sources: ESID Registry 20171117,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber Mode of inheritance for gene: PMS2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PMS2 were set to 7661930; 9488480; 15077197; 32086639; 16507833; 10763829; 32048120 Phenotypes for gene: PMS2 were set to Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Post-Meiotic Segregation 2 (PMS2) deficiency; Mismatch repair cancer syndrome 276300; Combined immunodeficiencies with associated or syndromic features; CSR defects and Hyper IgM (HIGM) syndromes; Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors