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Primary immunodeficiency

Gene: ITK

Green List (high evidence)

ITK (IL2 inducible T-cell kinase)
EnsemblGeneIds (GRCh38): ENSG00000113263
EnsemblGeneIds (GRCh37): ENSG00000113263
OMIM: 186973, Gene2Phenotype
ITK is in 5 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, 1:14 p.m. | Last Modified: 14 Oct 2020, 1:14 p.m.
Panel Version: 2.267
The following PubMed IDs were added to gene ITK (OMIM gene MIM#186973): 29867957. 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

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): ITK .PanelApp HGNC gene symbol check: ITK . IUIS Disease: ITK deficiency . IUIS Inheritance: AR .T cells: Normal, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: EBV associated B cell lymphoproliferation, lymphoma, Nl or 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.
Original metadata downloaded from ESID Registry. ESID_Gene_original: ITK, PanelApp HGNC gene symbol check: ITK, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency; Diseases of immune dysregulation / Hemophagocytic Lymphohistiocytosis (HLH) / ITK deficiency (HLH phenotype)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: ITK, GRID_Gene_Symbol: ITK, GRID_Transcript_ENS_Community submitted: ENST00000422843, GRID_Transcript_RefSeq: NM_005546.3, GRID_Transcript_ENS_used_on_Production: ENST00000422843
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Ellen McDonagh (Genomics England Curator)

Comment on list classification: Added by expert review, and ratd green by a second reviewer. Reports of 2 Turkish sisters, 3 members of an Arab family and one Moroccan case reported in OMIM.
Created: 3 Jun 2016, 1:49 p.m.

William Rae (University Hospital Southampton NHS Foundation Trust)

Green List (high evidence)

Phenotypes
EBV viraemia, HLH

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
  • GOSH PID v.8.0
  • Combined B and T cell defect v1.12
Phenotypes
  • Lymphoproliferative syndrome 1
  • Combined immunodeficiency
  • ITK deficiency (HLH phenotype)
  • EBV viraemia, HLH
  • EBV associated B cell lymphoproliferation, lymphoma, Nl or low IgG
  • Diseases of Immune Dysregulation
OMIM
186973
Clinvar variants
Variants in ITK
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: itk 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 ITK. Publications for gene ITK were updated from 19425169; 22289921; 21109689 to 29867957; 22289921; 21109689; 19425169 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 ITK.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to ITK.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to ITK.

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 ITK were set to Lymphoproliferative syndrome 1, Combined immunodeficiency, ITK deficiency (HLH phenotype), EBV viraemia, HLH, EBV associated B cell lymphoproliferation, lymphoma, Nl or 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 ITK. 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 ITK. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

13 Jun 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: ITK were set to Lymphoproliferative syndrome 1; Combined immunodeficiency; ITK deficiency (HLH phenotype); EBV viraemia, HLH

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to ITK. Panel: Primary immunodeficiency disorders Phenotypes for gene ITK were set to Lymphoproliferative syndrome 1, Combined immunodeficiency, ITK deficiency (HLH phenotype)

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene ITK were set to Lymphoproliferative syndrome 1

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to ITK. Panel: Primary immunodeficiency disorders Phenotypes for gene ITK were set to Lymphoproliferative syndrome 1

6 Apr 2018, Gel status: 4

Clear Sources

Louise Daugherty (Genomics England Curator)

ITK Source: GOSH PID 20171164 was removed from gene: ITK

6 Apr 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

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

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID 20171164 was added to ITK. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

ITK was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

ITK was created by Louise Daugherty