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Primary immunodeficiency

Gene: PMS2

Amber List (moderate evidence)

PMS2 (PMS1 homolog 2, mismatch repair system component)
EnsemblGeneIds (GRCh38): ENSG00000122512
EnsemblGeneIds (GRCh37): ENSG00000122512
OMIM: 600259, Gene2Phenotype
PMS2 is in 35 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
  • IUIS Classification December 2019
  • Expert Review Amber
  • IUIS Classification February 2018
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors
  • Mismatch repair cancer syndrome 276300
  • Post-Meiotic Segregation 2 (PMS2) deficiency
  • CSR defects and Hyper IgM (HIGM) syndromes
  • Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors
  • Combined immunodeficiencies with associated or syndromic features
OMIM
600259
Clinvar variants
Variants in PMS2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Feb 2020, Gel status: 2

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

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to PMS2. Mode of inheritance for gene PMS2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal Added phenotypes Recurrent infections, cafe-au-lait spots, lymphoma, colorectal carcinoma, brain tumors; Combined immunodeficiencies with associated or syndromic features for gene: PMS2 Publications for gene PMS2 were updated from 7661930; 15077197; 9488480; 10763829; 16507833 to 15077197; 32048120; 7661930; 9488480; 16507833; 10763829; 32086639

12 Jul 2018, Gel status: 2

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

4 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pms2 has been classified as Amber List (Moderate Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PMS2 were set to Mismatch repair cancer syndrome 276300, Post-Meiotic Segregation 2 (PMS2) deficiency, CSR defects and Hyper IgM (HIGM) syndromes, Recurrent infections, caf-au-lait spots, lymphoma, colorectal carcinoma, brain tumors, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to PMS2. Panel: Primary immunodeficiency disorders

9 May 2018, Gel status: 2

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

9 May 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for PMS2 were set to 7661930; 15077197; 9488480; 10763829; 16507833

9 May 2018, Gel status: 2

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for PMS2 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for PMS2 were set to Mismatch repair cancer syndrome 276300; Post-Meiotic Segregation 2 (PMS2) deficiency; CSR defects and Hyper IgM (HIGM) syndromes

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to PMS2. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to PMS2. Panel: Primary immunodeficiency disorders Phenotypes for gene PMS2 were set to Mismatch repair cancer syndrome, Post-Meiotic Segregation 2 (PMS2) deficiency, CSR defects and Hyper IgM (HIGM) syndromes

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PMS2 were set to Mismatch repair cancer syndrome

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

PMS2 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

PMS2 was created by Louise Daugherty