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Primary immunodeficiency

Gene: CTLA4

Green List (high evidence)

CTLA4 (cytotoxic T-lymphocyte associated protein 4)
EnsemblGeneIds (GRCh38): ENSG00000163599
EnsemblGeneIds (GRCh37): ENSG00000163599
OMIM: 123890, Gene2Phenotype
CTLA4 is in 6 panels

7 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, 12:40 p.m. | Last Modified: 14 Oct 2020, 12:40 p.m.
Panel Version: 2.241
The following PubMed IDs were added to entity CTLA4: 29729943;25213377;25329329. These publications have been associated with OMIM phenotype MIM#616100, which is listed for this entity, 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

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

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): CTLA4 .PanelApp HGNC gene symbol check: CTLA4 . IUIS Disease: CTLA4 deficiency (ALPSV) . IUIS Inheritance: AD .T cells: Reduced, .B cells: Decreased, .IUIS Other affected cells: N/A. IUIS Associated features: Autoimmune cytopenias, enteropathy, interstitial lung disease, extra-lymphoid lymphocytic infiltration recurrent infections . IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Regulatory T Cell Defects
Created: 2 Jul 2018, 10:35 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: CTLA-4, PanelApp HGNC gene symbol check: CTLA4, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency Diseases of immune dysregulation / Early-onset multi-organ autoimmune disease / Early-onset multi-organ autoimmune disease
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: CTLA4, GRID_Gene_Symbol: CTLA4, GRID_Transcript_ENS_Community submitted: ENST00000302823, GRID_Transcript_RefSeq: NM_005214.4, GRID_Transcript_ENS_used_on_Production: ENST00000302823
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Predominant phenotype is immune dysregulation; a broad range of autoimmune phenomena have been described along with polyclonal lymphocytic infiltrates. Susceptibility to infection and hypogammaglobulinaemia are not usually present in isolation

Ellen Thomas (Genomics England Curator)

Comment on list classification: Autoimmune condition leading to reduced T and B cells and hypogammaglobulinaemia.
Created: 16 May 2016, 1:46 p.m.

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: No expert review. No association with disease in Gen2Phen. Numerous variants reported in AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME, TYPE V in the two publications cited
Created: 13 May 2016, 7:27 a.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
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
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • CVID
  • hypogammaglobulinaemia
  • lymphadenopathy
  • T cell lymphopenia
  • enteropathy
  • interstitual lung disease
  • autoimmunity
  • Autoimmune lymphoproliferative syndrome, type V 616100
  • Autoimmune lymphoproliferative syndrome, type V
  • Combined immunodeficiency
  • Early-onset multi-organ autoimmune disease
  • Immune dysregulation
  • a broad range of autoimmune phenomena have been described along with polyclonal lymphocytic infiltrates. Susceptibility to infection and hypogammaglobulinaemia are not usually present in isolation
  • Autoimmune cytopenias, enteropathy, interstitial lung disease, extra-lymphoid lymphocytic infiltration recurrent infections
  • Diseases of Immune Dysregulation
OMIM
123890
Clinvar variants
Variants in CTLA4
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: ctla4 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to CTLA4. Publications for gene CTLA4 were updated from 25213377; 25329329 to 25213377; 25329329; 29729943 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 CTLA4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to CTLA4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to CTLA4.

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 CTLA4 were set to CVID, hypogammaglobulinaemia, lymphadenopathy, T cell lymphopenia, enteropathy, interstitual lung disease, autoimmunity, Autoimmune lymphoproliferative syndrome, type V 616100, Autoimmune lymphoproliferative syndrome, type V, Combined immunodeficiency, Early-onset multi-organ autoimmune disease, Immune dysregulation, a broad range of autoimmune phenomena have been described along with polyclonal lymphocytic infiltrates. Susceptibility to infection and hypogammaglobulinaemia are not usually present in isolation, Autoimmune cytopenias, enteropathy, interstitial lung disease, extra-lymphoid lymphocytic infiltration recurrent infections, 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 CTLA4. 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 CTLA4. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ctla4 has been classified as Green List (High Evidence).

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CTLA4 were set to CVID; hypogammaglobulinaemia; lymphadenopathy; T cell lymphopenia; enteropathy; interstitual lung disease; autoimmunity; Autoimmune lymphoproliferative syndrome, type V 616100; Autoimmune lymphoproliferative syndrome, type V; Combined immunodeficiency; Early-onset multi-organ autoimmune disease; Immune dysregulation; a broad range of autoimmune phenomena have been described along with polyclonal lymphocytic infiltrates. Susceptibility to infection and hypogammaglobulinaemia are not usually present in isolation

20 Apr 2018, Gel status: 4

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for CTLA4 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 CTLA4. Panel: Primary immunodeficiency disorders Phenotypes for gene CTLA4 were set to CVID, hypogammaglobulinaemia, lymphadenopathy, T cell lymphopenia, enteropathy, interstitual lung disease, autoimmunity, Autoimmune lymphoproliferative syndrome, type V 616100, Autoimmune lymphoproliferative syndrome, type V, Combined immunodeficiency, Early-onset multi-organ autoimmune disease

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CTLA4 were set to CVID, hypogammaglobulinaemia, lymphadenopathy, T cell lymphopenia, enteropathy, interstitual lung disease, autoimmunity, Autoimmune lymphoproliferative syndrome, type V 616100, Autoimmune lymphoproliferative syndrome, type V

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 CTLA4. Panel: Primary immunodeficiency disorders Model of inheritance for gene CTLA4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene CTLA4 were set to CVID, hypogammaglobulinaemia, lymphadenopathy, T cell lymphopenia, enteropathy, interstitual lung disease, autoimmunity, Autoimmune lymphoproliferative syndrome, type V 616100, Autoimmune lymphoproliferative syndrome, type V

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

CTLA4 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)

CTLA4 was created by Louise Daugherty