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Primary immunodeficiency

Gene: FOXP3

Green List (high evidence)

FOXP3 (forkhead box P3)
EnsemblGeneIds (GRCh38): ENSG00000049768
EnsemblGeneIds (GRCh37): ENSG00000049768
OMIM: 300292, Gene2Phenotype
FOXP3 is in 15 panels

5 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, 12:56 p.m. | Last Modified: 14 Oct 2020, 12:56 p.m.
Panel Version: 2.253
The following PubMed IDs were added to entity FOXP3: 29241729;18951619;30443250. These publications have been associated with OMIM phenotype MIM#304790, 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

Sophie Hambleton (Newcastle University)

Green List (high evidence)

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): FOXP3 .PanelApp HGNC gene symbol check: FOXP3 . IUIS Disease: IPEX, immune dysregulation, polyendocrinopathy, enteropathy X-linked . IUIS Inheritance: XL .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Autoimmune enteropathy, early onset diabetes, hyroiditis hemolytic anemia, thrombocytopenia, eczema, elevated IgE, IgA . IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Regulatory T Cell Defects
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed from Amber to Green enough evidence to support immune dysfunction
Created: 19 Jun 2018, 2:13 p.m.
Comment on publications: added publications to support gene-disease association
Created: 19 Jun 2018, 1:02 p.m.
Comment on phenotypes: added phenotype from orphanet and OMIM MIMid.Immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome is a severe congenital systemic autoimmune disease characterized by refractory diarrhea, endocrinopathies, cutaneous involvement, and infections.
Created: 19 Jun 2018, 12:55 p.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: FOXP3, PanelApp HGNC gene symbol check: FOXP3, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / IPEX / FOXP3 deficiency (IPEX)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: FOXP3, GRID_Gene_Symbol: FOXP3, GRID_Transcript_ENS_Community submitted: ENST00000376207, GRID_Transcript_RefSeq: NM_014009.3, GRID_Transcript_ENS_used_on_Production: ENST00000376207
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females
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
Phenotypes
  • Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, 304790
  • IPEX
  • FOXP3 deficiency (IPEX)
  • Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome
  • Autoimmune enteropathy, early onset diabetes, hyroiditis hemolytic anemia, thrombocytopenia, eczema, elevated IgE, IgA
  • Diseases of Immune Dysregulation
OMIM
300292
Clinvar variants
Variants in FOXP3
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: foxp3 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 FOXP3. Publications for gene FOXP3 were updated from 17635943; 16741580; 14671208; 11120765; 11295725 to 11295725; 29241729; 30443250; 17635943; 18951619; 11120765; 16741580; 14671208 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 FOXP3.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to FOXP3.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to FOXP3.

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 FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, 304790, IPEX, FOXP3 deficiency (IPEX), Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome, Autoimmune enteropathy, early onset diabetes, hyroiditis hemolytic anemia, thrombocytopenia, eczema, elevated IgE, IgA, Diseases of Immune Dysregulation

27 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: foxp3 has been classified as Green List (High Evidence).

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to FOXP3. 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 FOXP3. Panel: Primary immunodeficiency disorders

19 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: foxp3 has been classified as Green List (High Evidence).

19 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: FOXP3 were set to 17635943; 16741580; 14671208; 11120765; 11295725

19 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: FOXP3 were set to 17635943; 16741580; 14671208; 11120765; 11120765; 11295725

19 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, 304790; IPEX; FOXP3 deficiency (IPEX); Immune dysregulation polyendocrinopathy enteropathy X-linked syndrome

20 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked; IPEX; FOXP3 deficiency (IPEX)

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to FOXP3. 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 FOXP3. Panel: Primary immunodeficiency disorders Phenotypes for gene FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked (IPEX), FOXP3 deficiency (IPEX)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked (IPEX)

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to FOXP3. Panel: Primary immunodeficiency disorders Phenotypes for gene FOXP3 were set to Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked, Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked (IPEX)

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

FOXP3 Source: GOSH PID 20171151 was removed from gene: FOXP3

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to FOXP3. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

FOXP3 was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171151

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

FOXP3 was created by Louise Daugherty