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STRs in panel
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COVID-19 research

Gene: FOXN1

Green List (high evidence)

FOXN1 (forkhead box N1)
EnsemblGeneIds (GRCh38): ENSG00000109101
EnsemblGeneIds (GRCh37): ENSG00000109101
OMIM: 600838, Gene2Phenotype
FOXN1 is in 7 panels

7 reviews

Ivone Leong (Genomics England Curator)

Green List (high evidence)

IUIS: Inheritance - AR (causes Winged helix nude FOXN1 deficiency. Very low T cells and normal levels of B cells. Decreased Ig. Associated with severe infections; abnormal thymic epithelium, immunodeficiency; congenital alopecia, nail dystrophy; neural tube defect), AD (causes FOXN1 haploinsufficiency. Severe T cell lymphopenia at birth, normalised by adulthood and normal/low levels of B cells. Associated with recurrent, viral and bacterial respiratory tract infections; skin involvement (eczema, dermatitis), nail dystrophy).
Created: 15 Apr 2020, 12:09 p.m. | Last Modified: 15 Apr 2020, 12:09 p.m.
Panel Version: 0.103

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Publications

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)

I don't know

Added publication referenced by IUIS december 2019 update
Created: 28 Feb 2020, 8:49 p.m. | Last Modified: 28 Feb 2020, 8:49 p.m.
Panel Version: 2.36
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): FOXN1 .PanelApp HGNC gene symbol check: FOXN1 . IUIS Disease: Winged helix nudem FOXN1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Severe infections, abnormal thymic epithelium, immunodeficiency, congenital alopecia, nail dystrophy, neural tube defect. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Thymic Defects with Additional Congenital Anomalies
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: Changed from Amber to Green, single variant founder mutation (seen in Italian and Indian populations) but with functional analysis
Created: 18 Jun 2018, 9:38 a.m.
T-cell immunodeficiency, congenital alopecia, and nail dystrophy is a rare disorder, reported majorly in members of a large extended family from a Southern Italian community (PMID:15180707). Two sisters from Italy were the first to be reported with the features of severe combined immunodeficiency (SCID)/NUDE gene (PMID:8911612). Subsequent analysis of 263 Italian families revealed a founder mutation (PMID:11159512). The causative variant was a homozygous nonsense substitution (p.R255X), the resultant protein is likely to lack the DNA binding and transactivation domains resulting in loss-of function.
The FOXN1 p.R255X mutation observed in the PMID: 28636882 (2017) is an ancestral mutation reported in the Italian population. The presence of a homozygous nonsense mutation in FOXN1 gene, the same founder mutation in Italian population, was detected in the present family from South India. Probably, it is attributed to migration of people from the Italian peninsula to India mainly as merchants since Roman times. Functional analysis revealed lack of protein expression in the patients with the homozygous variant.
Created: 18 Jun 2018, 9:35 a.m.
added founder-effect tag
Created: 18 Jun 2018, 9:25 a.m.
Comment on publications: added publications to support FOXN1 loss of function variants cause Nude severe combined immunodeficiency
Created: 18 Jun 2018, 8:59 a.m.
This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Amber. The gene is present in the 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, 10:31 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: FOXN1, PanelApp HGNC gene symbol check: FOXN1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / NUDE/SCID / Winged-helix nude deficiency (FOXN1)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: FOXN1, GRID_Gene_Symbol: FOXN1, GRID_Transcript_ENS_Community submitted: ENST00000226247, GRID_Transcript_RefSeq: NM_003593.2, GRID_Transcript_ENS_used_on_Production: ENST00000226247
Created: 17 Apr 2018, 12:12 p.m.

Publications

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
T-B+ SCID, congenital alopecia, nail dystrophy

Publications

Peter Arkwright (Royal Manchester Foundation Trust)

Red List (low evidence)

Ellen McDonagh (Genomics England Curator)

Comment on list classification: As there is no consensus amoungst reviewers, this gene has been made amber. It is a confirmed DD gene for Alopecia and T-cell immunodeficiency.
Created: 20 May 2016, 2:17 p.m.

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
we are now trying to validate one of these but more CID than classic SCID
Created: 12 Jan 2016, 4:09 p.m.

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • IUIS Classification December 2024
Phenotypes
  • Nude severe combined immunodeficiency
  • T-cell immunodeficiency, congenital alopecia, and nail dystrophy
  • T-B+ SCID
  • Severe infections, abnormal thymic epithelium, immunodeficiency, congenital alopecia, nail dystrophy, neural tube defect
  • T-B+ SCID, congenital alopecia, nail dystrophy, 601705
  • Combined immunodeficiencies with associated or syndromic features
OMIM
600838
Clinvar variants
Variants in FOXN1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

15 Apr 2020, Gel status: 3

Added New Source, Set mode of inheritance

Ivone Leong (Genomics England Curator)

Source IUIS Classification December 2024 was added to FOXN1. Mode of inheritance for gene FOXN1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

1 Apr 2020, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: FOXN1 was added gene: FOXN1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,SCID v1.6,IUIS Classification February 2018 Mode of inheritance for gene: FOXN1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FOXN1 were set to 28636882; 15180707; 21507891; 11159512; 31447097; 10206641; 28077132; 29593714 Phenotypes for gene: FOXN1 were set to Nude severe combined immunodeficiency; T-cell immunodeficiency, congenital alopecia, and nail dystrophy; T-B+ SCID; Severe infections, abnormal thymic epithelium, immunodeficiency, congenital alopecia, nail dystrophy, neural tube defect; T-B+ SCID, congenital alopecia, nail dystrophy, 601705; Combined immunodeficiencies with associated or syndromic features