COVID-19 research

Gene: STAT1

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

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

Green List (high evidence)

Monoallelic gain-of-function causes a combined immunodeficiency with prominent chronic mucocutaneous candidiasis and autoimmunity.
Monoallelic hypomorphic mutation causes susceptibility to mycobacterial disease (MSMD).
Biallelic loss of function causes susceptibility to both mycobacterial and viral disease.

Evidence for each of these 3 aetiologies is strong.

Created: 11 Jun 2018, 12:21 p.m.

Mode of inheritance
BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal

Mode of pathogenicity
Other

Comment on list classification: STAT1 is associated with Immunodeficiency 31A,B, and C in OMIM.
More than 3 unrelated cases reported for each disorder. Both gain and loss of function variants reported (gain - Liu et al. (2011) (PMID: 21727188), Soltesz et al. (2013) (PMID: 23709754), Sampaio et al. (2013) (PMID: 23541320) , Uzel et al. (2013) (PMID: 23534974), Carey et al (2018) (PMID: 29702748) and loss - Mork et al 2015 (PMID: 26513235).

Created: 1 May 2018, 4:15 p.m.

Comment on mode of pathogenicity: Both gain of function and loss of function variants reported. See rating review.

Created: 1 May 2018, 4:15 p.m.

Comment on publications: Added relevant publications.

Created: 1 May 2018, 4:14 p.m.

Comment on phenotypes: Added MIM IDs

Created: 1 May 2018, 3:09 p.m.

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): STAT1 .PanelApp HGNC gene symbol check: STAT1 . IUIS Disease: STAT1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: T and NK cells and monocytes. IUIS Associated features: Severe viral infections, mycobacterial infection. IUIS Major category: Defects in Intrinsic and Innate Immunity. IUIS Subcategory: Predisposition to Severe Viral Infection. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): STAT1 .PanelApp HGNC gene symbol check: STAT1 . IUIS Disease: STAT1 . IUIS Inheritance: AD GOF .T cells: Normal , .B cells: N/A, .IUIS Other affected cells: T cells, B cells, monocytes. IUIS Associated features: CMC, various fungal, bacterial and viral (HSV) infections, auto-immunity (thyroiditis, diabetes, cytopenias), enteropathy. IUIS Major category: Defects in Intrinsic and Innate Immunity. IUIS Subcategory: Predisposition to Mucocutaneous Candidiasis. // OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): STAT1 .PanelApp HGNC gene symbol check: STAT1 . IUIS Disease: STAT1 deficiency . IUIS Inheritance: AD .T cells: Variable, .B cells: N/A, .IUIS Other affected cells: M + L. IUIS Associated features: Susceptibility to mycobacteria, Salmonella, . IUIS Major category: Defects in Intrinsic and Innate Immunity. IUIS Subcategory: Mendelian Susceptibility to mycobacterial disease (MSMD)

Created: 2 Jul 2018, 11 a.m.

Comment on mode of pathogenicity: from Expert review comment: Monoallelic gain-of-function causes a combined immunodeficiency with prominent chronic mucocutaneous candidiasis and autoimmunity. Monoallelic hypomorphic mutation causes susceptibility to mycobacterial disease (MSMD). Biallelic loss of function causes susceptibility to both mycobacterial and viral disease. Evidence for each of these 3 aetiologies is strong.

Created: 13 Jun 2018, 10:37 a.m.

Comment on mode of inheritance: updated MOI from external expert review

Created: 13 Jun 2018, 10:37 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: 19 Apr 2018, 2:24 p.m.

Original metadata downloaded from ESID Registry. ESID_Gene_original: STAT1, PanelApp HGNC gene symbol check: STAT1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency; Defects in innate immunity / Chronic mucocutaneous candidiasis (CMC) / Chronic mucocutaneous candidiasis (CMC); Phagocytic disorders / Defects with susceptibility to mycobacterial infection (MSMD) / Defects with susceptibility to mycobacterial infection (MSMD)

Created: 17 Apr 2018, 12:29 p.m.

Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: STAT1, GRID_Gene_Symbol: STAT1, GRID_Transcript_ENS_Community submitted: ENST00000361099, GRID_Transcript_RefSeq: NM_007315.3, GRID_Transcript_ENS_used_on_Production: ENST00000361099

Created: 17 Apr 2018, 12:12 p.m.