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Primary immunodeficiency

Gene: PIK3CD

Green List (high evidence)

PIK3CD (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta)
EnsemblGeneIds (GRCh38): ENSG00000171608
EnsemblGeneIds (GRCh37): ENSG00000171608
OMIM: 602839, Gene2Phenotype
PIK3CD is in 7 panels

10 reviews

Arina Puzriakova (Genomics England Curator)

Added 'for-review' tag as the MOI has changed since previous sign-off of this panel (version 2.1) and requires review by the Specialist Test Group.
Created: 21 Oct 2020, 4:34 p.m. | Last Modified: 21 Oct 2020, 4:34 p.m.
Panel Version: 2.368

Ivone Leong (Genomics England Curator)

Comment on mode of inheritance: Updated MOI from Monoallelic to Both Monoallelic and biallelic based on expert review and evidence provided by Zornitza Stark (Australian Genomics).
Created: 15 Apr 2020, 2:29 p.m. | Last Modified: 15 Apr 2020, 2:29 p.m.
Panel Version: 2.64

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Note recent reports of bi-allelic variants causing disease.
Created: 12 Apr 2020, 4:50 a.m. | Last Modified: 12 Apr 2020, 4:50 a.m.
Panel Version: 2.51

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Severe bacterial infections; autoimmunity

Publications

Ilenia Simeoni (Addenbrooke's Hospital Cambridge Biomedical Campus)

Green List (high evidence)

Agree with green gene.
This gene is included in our exome panel GEMINI
Created: 14 Oct 2019, 10:01 a.m. | Last Modified: 14 Oct 2019, 10:01 a.m.
Panel Version: 1.132

Publications

Variants in this GENE are reported as part of current diagnostic practice

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): PIK3CD GOF .PanelApp HGNC gene symbol check: PIK3CD . IUIS Disease: PIK3CD mutation . IUIS Inheritance: AD .T cells: Normal, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Severe bacterial infections; decreased or absent pro-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, 10:35 a.m.
Comment on phenotypes: Added phenotypes suggested from external expert review.
Created: 13 Jun 2018, 2:35 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: PIK3CD (PI3K-delta), PanelApp HGNC gene symbol check: PIK3CD, 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 / Unclassified antibody deficiency / Unclassified antibody deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: PIK3CD, GRID_Gene_Symbol: PIK3CD, GRID_Transcript_ENS_Community submitted: ENST00000377346, GRID_Transcript_RefSeq: NM_005026.3, GRID_Transcript_ENS_used_on_Production: ENST00000377346
Created: 17 Apr 2018, 12:12 p.m.

William Rae (University Hospital Southampton NHS Foundation Trust)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

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
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
sinopulmonary infections, dysgammaglobulinaemia, lymphadenopathy, nodular lymphoid hyperplasia and herpesviremia

Publications

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Three positive expert reviews. Not associated with disease on Gen2Phen. Numerous disease associated variants reported in the publications.
Created: 11 May 2016, 10:07 a.m.

Details

Mode of Inheritance
BOTH monoallelic and biallelic, 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
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • Immunodeficiency 14,615513
  • Combined immunodeficiency
  • Unclassified antibody deficiency
  • Activated PI3K-delta syndrome (APDS)
  • sinopulmonary infections, dysgammaglobulinaemia, lymphadenopathy, nodular lymphoid hyperplasia and herpesviremia
  • Severe bacterial infections
  • decreased or absent pro-B cells, EBV
  • Predominantly Antibody Deficiencies
Tags
for-review
OMIM
602839
Clinvar variants
Variants in PIK3CD
Penetrance
None
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

21 Oct 2020, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: PIK3CD.

15 Apr 2020, Gel status: 3

Set mode of inheritance

Ivone Leong (Genomics England Curator)

Mode of inheritance for gene: PIK3CD was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

15 Apr 2020, Gel status: 3

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: PIK3CD were set to 24165795; 24136356; 29226301

28 Feb 2020, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: PIK3CD were set to 24165795; 24136356

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to PIK3CD.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to PIK3CD.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to PIK3CD.

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 penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PIK3CD were set to Immunodeficiency 14,615513, Combined immunodeficiency, Unclassified antibody deficiency, Activated PI3K-delta syndrome (APDS), sinopulmonary infections, dysgammaglobulinaemia, lymphadenopathy, nodular lymphoid hyperplasia and herpesviremia, Severe bacterial infections, decreased or absent pro-B cells, EBV, Predominantly Antibody Deficiencies

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to PIK3CD. 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 PIK3CD. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pik3cd has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: PIK3CD were set to Immunodeficiency 14,615513; Combined immunodeficiency; Unclassified antibody deficiency; Activated PI3K-delta syndrome (APDS); sinopulmonary infections, dysgammaglobulinaemia, lymphadenopathy, nodular lymphoid hyperplasia and herpesviremia

20 Apr 2018, Gel status: 4

Set mode of pathogenicity

Louise Daugherty (Genomics England Curator)

Mode of pathogenicity for PIK3CD was changed to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for PIK3CD were set to Immunodeficiency 14,615513; Combined immunodeficiency; Unclassified antibody deficiency; Activated PI3K-delta syndrome (APDS)

20 Apr 2018, Gel status: 4

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for PIK3CD was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to PIK3CD. Panel: Primary immunodeficiency disorders Phenotypes for gene PIK3CD were set to Immunodeficiency 14, 615513, Combined immunodeficiency, Unclassified antibody deficiency, Activated PI3K-delta syndrome (APDS)

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PIK3CD were set to Immunodeficiency 14, 615513

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 PIK3CD. Panel: Primary immunodeficiency disorders Model of inheritance for gene PIK3CD was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene PIK3CD were set to Immunodeficiency 14, 615513

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

PIK3CD 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)

PIK3CD was created by Louise Daugherty