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Primary immunodeficiency

Gene: NFAT5

Red List (low evidence)

NFAT5 (nuclear factor of activated T-cells 5)
EnsemblGeneIds (GRCh38): ENSG00000102908
EnsemblGeneIds (GRCh37): ENSG00000102908
OMIM: 604708, Gene2Phenotype
NFAT5 is in 3 panels

4 reviews

Eleanor Williams (Genomics England Curator)

The following PubMed IDs were added to gene NFAT5 (OMIM gene MIM#604708): 25667416. 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

Sophie Hambleton (Newcastle University)

Red List (low evidence)

One case only described
Created: 29 Jun 2018, 2:51 p.m.

Sarah Leigh (Genomics England Curator)

Red List (low evidence)

Comment on list classification: This rating of this gene has been returned to red. The amber rating was made in error as only one immunodeficiency associated variant has been reported in this gene.
Created: 26 Sep 2018, 2:30 p.m.
Not associated with a phenotype in OMIM or in Gen2Phen. No variants reported, however, haploinsufficiency of NFAT5 was reported in young man with autoimmune enterocolopathy and unexplained infections revealing evidence of immunodeficiency, including IgG subclass deficiency, impaired Ag-induced lymphocyte proliferation, reduced cytokine production by CD8(+) T lymphocytes, and decreased numbers of NK cells (PMID 25667416).
NFAT5 is one of 8 genes (NFAT5, MIR1538, NQO1, NOB1, WWP2, MIR140, CLEC18A, and PDXDC2) located in a 559-kilobase deletion within 16q22.1 (PMID 25667416), none of the other genes appear to have any association with immunodeficiency and are not listed on this panel.
Based on this evidence in consultation with Helen Britain (Clinical Fellow, Genomics England), this gene has been promoted to amber, with a "watchlist" tag applied as it appears that changes in this gene could potentially be relevant to this panel.
Created: 2 May 2018, 1:38 p.m.

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

watch tag added - there is supportive evidence in terms of cellular studies in mice that partially reproduce the immune phenotype with haploinsufficiency of this gene, Watchlist tag added in relation for further evidence of CNV / SNVs to promote it to green.
Created: 26 Sep 2018, 2:37 p.m.
Comment on list classification: Changed from Amber to Red. Only one published case with immunodeficiency to date. Gene is pertinent on Victorian Clinical Genetics Services panel and GRID for Immunological disorders. Request evidences from Victorian Clinical Genetics Services and GRID.
Created: 4 Jul 2018, 4:03 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): NFAT5 .PanelApp HGNC gene symbol check: NFAT5 . IUIS Disease: NFAT5 haploinsufficiency . IUIS Inheritance: AD .T cells: CD8 and CD4 T cells may be decreased, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: IBD, recurrent sinopulmonary infections. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Immune Dysregulation with Colitis
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 supplied by GRID. GRID Gene Symbol HGNC PanelApp check: NFAT5, GRID_Gene_Symbol: NFAT5, GRID_Transcript_ENS_Community submitted: ENST00000432919, GRID_Transcript_RefSeq: NM_138714.3, GRID_Transcript_ENS_used_on_Production: ENST00000432919
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Other
  • IUIS Classification December 2019
  • Expert Review Red
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • GRID V2.0
Phenotypes
  • Diseases of Immune Dysregulation
  • IBD, recurrent sinopulmonary infections
  • NFAT5 haploinsufficieny
Tags
watchlist
OMIM
604708
Clinvar variants
Variants in NFAT5
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Oct 2020, Gel status: 1

Added New Source, Set publications

Eleanor Williams (Genomics England Curator)

Source Other was added to NFAT5. Publications for gene NFAT5 were updated from 32048120; 32086639 to 32086639; 25667416; 32048120

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to NFAT5. Added phenotypes IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation for gene: NFAT5 Publications for gene NFAT5 were updated from to 32048120; 32086639

26 Sep 2018, Gel status: 1

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: nfat5 has been classified as Red List (Low Evidence).

18 Sep 2018, Gel status: 2

Added Tag

Sarah Leigh (Genomics England Curator)

Tag watchlist tag was added to gene: NFAT5.

18 Sep 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: nfat5 has been classified as Amber List (Moderate Evidence).

12 Jul 2018, Gel status: 1

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.

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: nfat5 has been classified as Red List (Low Evidence).

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: nfat5 has been classified as Red List (Low Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene NFAT5 were set to NFAT5 haploinsufficieny, IBD, recurrent sinopulmonary infections, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to NFAT5. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to NFAT5. Panel: Primary immunodeficiency disorders

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to NFAT5. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene NFAT5 were set to NFAT5 haploinsufficieny

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

NFAT5 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

NFAT5 was created by Louise Daugherty