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Primary immunodeficiency

Gene: PIK3R1

Green List (high evidence)

PIK3R1 (phosphoinositide-3-kinase regulatory subunit 1)
EnsemblGeneIds (GRCh38): ENSG00000145675
EnsemblGeneIds (GRCh37): ENSG00000145675
OMIM: 171833, Gene2Phenotype
PIK3R1 is in 17 panels

8 reviews

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

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 enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
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 enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): PIK3R1 .PanelApp HGNC gene symbol check: PIK3R1 . IUIS Disease: PIK3R1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Severe bacterial infections, decreased or absent pro-B cells. IUIS Major category: Predominantly Antibody Deficiencies. IUIS Subcategory: Severe Reduction in All Serum Immunoglobulin Isotypes with Profoundly Decreased or Absent B Cells, Agammaglobulinemia. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): PIK3R1 .PanelApp HGNC gene symbol check: PIK3R1 . IUIS Disease: PIK3R1 deficiency . IUIS Inheritance: AD .T cells: Very low, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Severe bacterial infections, pro-B cells present and low numbers of memory B cells, EBV. 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: 2 Jul 2018, 10:58 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: PIK3R1, PanelApp HGNC gene symbol check: PIK3R1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency; Combined immunodeficiencies / Combined immunodeficiency (CID) / Activated PI3K-delta syndrome (APDS); Predominantly antibody disorders / Agammaglobulinemias / Agammaglobulinemia
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: PIK3R1, GRID_Gene_Symbol: PIK3R1, GRID_Transcript_ENS_Community submitted: ENST00000521381, GRID_Transcript_RefSeq: NM_181523.2, GRID_Transcript_ENS_used_on_Production: ENST00000521381
Created: 17 Apr 2018, 12:12 p.m.

William Rae (University Hospital Southampton NHS Foundation Trust)

Green List (high evidence)

Christopher Duncan (Newcastle University)

Green List (high evidence)

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal

Phenotypes
agammaglobulinaemia (AR); immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD)

Publications

Peter Arkwright (Royal Manchester Foundation Trust)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Five positive expert reviews. Disease association on Gen2Phen. LOF variant found in one homozygous Agammaglobulinemia 7 patient and more than three LOF variants found in unrelated Immunodeficiency 36 patients
Created: 11 May 2016, 10:26 a.m.
Comment on mode of inheritance: From omim for Agammaglobulinemia 7, autosomal recessive
Created: 10 May 2016, 9:55 a.m.

Details

Mode of Inheritance
BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • ESID Registry 20171117
  • GRID V2.0
  • GOSH PID v.8.0
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • Immunodeficiency 36
  • Agammaglobulinemia 7, autosomal recessive, 615214
  • SHORT syndrome, 269880
  • Immunodeficiency 36, 616005
  • Agammaglobulinemia 7
  • Immunodeficiency 36
  • Combined immunodeficiency
  • Activated PI3K-delta syndrome (APDS)
  • Agammaglobulinemia
  • immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD)
  • Severe bacterial infections, decreased or absent pro-B cells
  • Predominantly Antibody Deficiencies
  • Severe bacterial infections, pro-B cells present and low numbers of memory B cells, EBV
OMIM
171833
Clinvar variants
Variants in PIK3R1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to PIK3R1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to PIK3R1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to PIK3R1.

12 Jul 2018, Gel status: 4

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: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: PIK3R1 were set to Immunodeficiency 36; Agammaglobulinemia 7, autosomal recessive, 615214; SHORT syndrome, 269880; Immunodeficiency 36, 616005; Agammaglobulinemia 7; Immunodeficiency 36; Combined immunodeficiency; Activated PI3K-delta syndrome (APDS); Agammaglobulinemia; immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD); Severe bacterial infections, decreased or absent pro-B cells; Predominantly Antibody Deficiencies; Severe bacterial infections, pro-B cells present and low numbers of memory B cells, EBV

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to PIK3R1. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to PIK3R1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pik3r1 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: PIK3R1 were set to Immunodeficiency 36; Agammaglobulinemia 7, autosomal recessive, 615214; SHORT syndrome, 269880; Immunodeficiency 36, 616005; Agammaglobulinemia 7; Immunodeficiency 36; Combined immunodeficiency; Activated PI3K-delta syndrome (APDS); Agammaglobulinemia; immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD)

13 Jun 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: PIK3R1 were set to Immunodeficiency 36; Agammaglobulinemia 7, autosomal recessive, 615214; SHORT syndrome, 269880; Immunodeficiency 36, 616005; Agammaglobulinemia 7; Immunodeficiency 36; Combined immunodeficiency; Activated PI3K-delta syndrome (APDS); Agammaglobulinemia; immunodeficiency with hypogammaglobulinaemia, lymphoproliferation and inflammatory disease (AD)

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for PIK3R1 were set to Immunodeficiency 36; Agammaglobulinemia 7, autosomal recessive, 615214; SHORT syndrome, 269880; Immunodeficiency 36, 616005; Agammaglobulinemia 7; Immunodeficiency 36; Combined immunodeficiency; Activated PI3K-delta syndrome (APDS); Agammaglobulinemia

20 Apr 2018, Gel status: 4

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for PIK3R1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to PIK3R1. Panel: Primary immunodeficiency disorders Phenotypes for gene PIK3R1 were set to Immunodeficiency 36, Agammaglobulinemia 7, autosomal recessive, 615214, SHORT syndrome, 269880, Immunodeficiency 36, 616005, Agammaglobulinemia 7, Immunodeficiency 36, Immunodeficiency 36, Combined immunodeficiency, Activated PI3K-delta syndrome (APDS), Agammaglobulinemia

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PIK3R1 were set to Immunodeficiency 36, Agammaglobulinemia 7, autosomal recessive, 615214, SHORT syndrome, 269880, Immunodeficiency 36, 616005, Agammaglobulinemia 7, Immunodeficiency 36, Immunodeficiency 36

17 Apr 2018, Gel status: 4

Added New Source, Set mode of inheritance, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to PIK3R1. Panel: Primary immunodeficiency disorders Model of inheritance for gene PIK3R1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene PIK3R1 were set to Immunodeficiency 36, Agammaglobulinemia 7, autosomal recessive, 615214, SHORT syndrome, 269880, Immunodeficiency 36, 616005, Agammaglobulinemia 7, Immunodeficiency 36

6 Apr 2018, Gel status: 4

Clear Sources

Louise Daugherty (Genomics England Curator)

PIK3R1 Source: GOSH PID 20171177 was removed from gene: PIK3R1

6 Apr 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to PIK3R1. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 4

Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

GOSH PID 20171177 was added to PIK3R1. Panel: Primary immunodeficiency disorders Model of inheritance for gene PIK3R1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

PIK3R1 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, A- or hypo-gammaglobulinaemia v1.25

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

PIK3R1 was created by Louise Daugherty