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Primary immunodeficiency

Gene: PRKCD

Green List (high evidence)

PRKCD (protein kinase C delta)
EnsemblGeneIds (GRCh38): ENSG00000163932
EnsemblGeneIds (GRCh37): ENSG00000163932
OMIM: 176977, Gene2Phenotype
PRKCD is in 3 panels

6 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 1:41 p.m. | Last Modified: 14 Oct 2020, 1:41 p.m.
Panel Version: 2.296
The following PubMed IDs were added to gene PRKCD (OMIM gene MIM#176977): 27541826;23666743;23319571. These publications have been associated with the gene by the immunedysregulation subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
The following PubMed IDs were added to gene PRKCD (OMIM gene MIM#176977): 23722905;25842288;19075392. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:33 a.m. | Last Modified: 13 Oct 2020, 9:33 a.m.
Panel Version: 2.207

Publications

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

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)

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 3 variants identified in 3 unrelated cases, together with supportive in vitro evidence.
Created: 9 May 2018, 1:03 p.m.

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): PRKCD .PanelApp HGNC gene symbol check: PRKCD . IUIS Disease: PRKCD deficiency . IUIS Inheritance: AR .T cells: Nl number, low Treg, high CD4, poor function, .B cells: Low memory B cells, high CD5 B cells, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent infections, EBV chronic infection, lymphoproliferation, SLE-like autoimmunity (nephrotic and antiphospholipid syndromes), low IgG. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Susceptibility to EBV and Lymphoproliferative Conditions
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: PRKCD, PanelApp HGNC gene symbol check: PRKCD, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Autoimmune lymphoproliferative syndrome (ALPS) / Autoimmune lymphoproliferative syndrome (ALPS); 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: PRKCD, GRID_Gene_Symbol: PRKCD, GRID_Transcript_ENS_Community submitted: ENST00000394729, GRID_Transcript_RefSeq: NM_006254.3, GRID_Transcript_ENS_used_on_Production: ENST00000394729
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Autoimmune lymphoproliferative syndrome, type III 615559
  • Immunodeficiency, common variable, 9
  • Autoimmune lymphoproliferative syndrome (ALPS)
  • Unclassified antibody deficiency
  • Recurrent infections, EBV chronic infection, lymphoproliferation, SLE-like autoimmunity (nephrotic and antiphospholipid syndromes), low IgG
  • Diseases of Immune Dysregulation
OMIM
176977
Clinvar variants
Variants in PRKCD
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

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

13 Oct 2020, Gel status: 1

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene PRKCD were updated from 23319571; 27541826; 23666743; 23430113 to 19075392; 23430113; 25842288; 23722905; 23319571; 27541826; 23666743

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to PRKCD. Publications for gene PRKCD were updated from 23319571; 23666743; 23430113 to 23319571; 27541826; 23666743; 23430113 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to PRKCD.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to PRKCD.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to PRKCD.

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 PRKCD were set to Autoimmune lymphoproliferative syndrome, type III 615559, Immunodeficiency, common variable, 9, Autoimmune lymphoproliferative syndrome (ALPS), Unclassified antibody deficiency, Recurrent infections, EBV chronic infection, lymphoproliferation, SLE-like autoimmunity (nephrotic and antiphospholipid syndromes), low IgG, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

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

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

9 May 2018, Gel status: 3

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

9 May 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for PRKCD were set to 23319571; 23666743; 23430113

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for PRKCD were set to Autoimmune lymphoproliferative syndrome, type III 615559; Immunodeficiency, common variable, 9; Autoimmune lymphoproliferative syndrome (ALPS); Unclassified antibody deficiency

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to PRKCD. 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 PRKCD. Panel: Primary immunodeficiency disorders Phenotypes for gene PRKCD were set to Immunodeficiency, common variable, 9, Autoimmune lymphoproliferative syndrome (ALPS), Unclassified antibody deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene PRKCD were set to Immunodeficiency, common variable, 9

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

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

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

PRKCD was created by Louise Daugherty