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STRs in panel
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COVID-19 research

Gene: NFAT5

Green List (high evidence)

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

3 reviews

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.


Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
  • Expert Review Green
  • IUIS Classification February 2018
  • IUIS Classification December 2019
  • GRID V2.0
  • Victorian Clinical Genetics Services
  • IUIS Classification December 2019
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • GRID V2.0
  • NFAT5 haploinsufficieny
  • IBD, recurrent sinopulmonary infections
  • Diseases of Immune Dysregulation
Clinvar variants
Variants in NFAT5
Panels with this gene

History Filter Activity

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to NFAT5. Added phenotypes NFAT5 haploinsufficieny; IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation for gene: NFAT5 Rating Changed from Red List (low evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 1

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

Ellen McDonagh (Genomics England Curator)

gene: NFAT5 was added gene: NFAT5 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018 Mode of inheritance for gene: NFAT5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: NFAT5 were set to 32086639; 32048120 Phenotypes for gene: NFAT5 were set to NFAT5 haploinsufficieny; IBD, recurrent sinopulmonary infections; Diseases of Immune Dysregulation