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Primary immunodeficiency

Gene: PTEN

Amber List (moderate evidence)

PTEN (phosphatase and tensin homolog)
EnsemblGeneIds (GRCh38): ENSG00000171862
EnsemblGeneIds (GRCh37): ENSG00000171862
OMIM: 601728, Gene2Phenotype
PTEN is in 55 panels

5 reviews

Arina Puzriakova (Genomics England Curator)

- PMID: 32588888 (2020) - Sequencing of the T-cell receptor variable-region β-chain using peripheral blood from patients with PTEN hamartoma tumour syndrome (PHTS), revealed that patients with PTEN variants had a skewed T- and B-cell gene repertoire, characterised by increased prevalence of high-frequency clones, compared to PTEN wild-type population.

Pten knock-in murine models similarly exhibited skewed immune repertoire compositions. Mutants also displayed B-cell hyperactivation and T-cell hyper-reactivity upon Toll-like-receptor stimulation. Decreases in nuclear but not cytoplasmic Pten levels were associated with reduced expression of the autoimmune regulator (Aire), indicating that nuclear PTEN likely regulates Aire expression via its emerging role in splicing regulation.

Authors speculate that such disruptions in central immune tolerance processes due to PTEN variants may impact individual stress responses and therefore predisposition to chronic inflammation, autoimmunity and cancer.
Created: 22 Sep 2020, 2:17 p.m. | Last Modified: 22 Sep 2020, 2:17 p.m.
Panel Version: 2.193

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Sophie Hambleton (Newcastle University)

I don't know

Agree amber rating
Created: 23 Oct 2019, 7:11 a.m. | Last Modified: 23 Oct 2019, 7:11 a.m.
Panel Version: 1.132

Kimberly Gilmour (Great Ormond Street Hopsital)

I don't know

agree with all the Amber genes
Created: 25 Sep 2019, 1:49 p.m. | Last Modified: 25 Sep 2019, 1:49 p.m.
Panel Version: 1.115

Tracy Briggs (Manchester Genomic Medicine Centre)

I don't know

The amber genes are covered on our targeted exome, we feel that these should be covered in the testing
Created: 25 Sep 2019, 1:44 p.m. | Last Modified: 25 Sep 2019, 1:44 p.m.
Panel Version: 1.114

Louise Daugherty (Genomics England Curator)

I don't know

Cowden (macrocephaly, variable GDD, skin features, malignancy risk) - some patients reported to have primary immunodef / hypogammaglob. / lymphopaenia / T&B cell abn. / susceptibility to infections). Green association - relevant phenotype?
Created: 26 Sep 2019, 3:58 p.m. | Last Modified: 26 Sep 2019, 3:58 p.m.
Panel Version: 1.130
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is only enough evidence to rate this gene Amber.
Created: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is only enough evidence to rate this gene Amber
Created: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
Comment on list classification: Changed from Red to Amber. As discussed with the GMS Immunology Specialist Test Group webex call 28th March 2019: The Specialist Test Group all agreed that there is only enough evidence to rate this gene Amber- publication evidence supplied by expert
Created: 15 Aug 2019, 3:33 p.m. | Last Modified: 16 Aug 2019, 9:07 a.m.
Panel Version: 1.51
Comment on publications: publication added to support upgrading gene to Amber- suggested by Sophie Hambleton in the GMS Immunological Specialist Test Group webex call 28th March 2019
Created: 29 Mar 2019, 12:56 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): PTEN .PanelApp HGNC gene symbol check: PTEN . IUIS Disease: PTEN Deficiency . IUIS Inheritance: AD .T cells: Normal, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Lymphoproliferation, Autoimmunity. IUIS Major category: Predominantly Antibody Deficiencies. IUIS Subcategory: Severe Reduction in at Least 2 Serum Immunoglobulin Isotypes with Normal or Low Number of B Cells, CVID Phenotype
Created: 6 Jul 2018, 12:33 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • IUIS Classification December 2019
  • North West GLH
  • London North GLH
  • NHS GMS
  • Expert Review Amber
  • IUIS Classification February 2018
Phenotypes
  • Recurrent infections, Lymphoproliferation, Autoimmunity
  • developmental delay
  • Predominantly Antibody Deficiencies
  • Lymphoproliferation, Autoimmunity
OMIM
601728
Clinvar variants
Variants in PTEN
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Feb 2020, Gel status: 2

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to PTEN. Added phenotypes Recurrent infections, Lymphoproliferation, Autoimmunity; developmental delay; Predominantly Antibody Deficiencies for gene: PTEN Publications for gene PTEN were updated from 27426521 to 32048120; 27426521; 32086639

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to PTEN.

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to PTEN.

17 Sep 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to PTEN.

15 Aug 2019, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

29 Mar 2019, Gel status: 1

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: PTEN was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

29 Mar 2019, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: PTEN were set to

12 Jul 2018, Gel status: 1

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.

1 Jul 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PTEN were set to Lymphoproliferation, Autoimmunity, Predominantly Antibody Deficiencies

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

PTEN was added to Primary immunodeficiency disorders panel. Sources: IUIS Classification February 2018

26 Jun 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

PTEN was created by Louise Daugherty