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COVID-19 research

Gene: TMEM173

Green List (high evidence)

TMEM173 (transmembrane protein 173)
EnsemblGeneIds (GRCh38): ENSG00000184584
EnsemblGeneIds (GRCh37): ENSG00000184584
OMIM: 612374, Gene2Phenotype
TMEM173 is in 6 panels

7 reviews

Ivone Leong (Genomics England Curator)

Green List (high evidence)

IUIS: Inheritance - AR (causes STING-associated vasculopathy, infantile-onset (SAVI). STING activates both the NF-kappa-B and IRF3 transcription pathways to induce expression of IFN. Associated with skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL).
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

Ellen McDonagh (Genomics England Curator)

Comment on list classification: Promoted to Green as clear evidence for this gene in viral susceptibility.
Created: 1 Apr 2020, 10:15 a.m. | Last Modified: 1 Apr 2020, 10:15 a.m.
Panel Version: 0.35
Additional evidence added to the publication list, provided by Abdelazeem Elhabyan. Comments from Abdelazeem Elhabyan: GenBank - https://www.ncbi.nlm.nih.gov/gene?term=(human%5BOrganism%5D)%20AND%20TMEM173%5BGene%20Name%5D) This gene encodes a five transmembrane protein that functions as a major regulator of the innate immune response to viral and bacterial infections. The encoded protein is a pattern recognition receptor that detects cytosolic nucleic acids and transmits signals that activate type I interferon responses.

Hypothesis:
This gene is involved in interferon 1 pathway which is directly related to viral innate immune response. Upregulation may be associated with a protective effect or autoinflammatory response with aggravating effect. This is to be determined by clinical trials.

Highest organ of expression is the lung in genbank (Pneumonia caused by corona) RPKM ,\mean is 37

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069765/

Extracellular vesicles released by virally infected cells(HSV) that carry STING can induce protective effect against viral replication in neighbouring non infected cells
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146713/

Virulent Poxviruses Inhibit DNA Sensing by Preventing STING Activation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923072/
The gene is involved in acute pancreatitis in mice
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112120/
Created: 1 Apr 2020, 10:14 a.m. | Last Modified: 1 Apr 2020, 10:14 a.m.
Panel Version: 0.34
This gene is Green on the Primary immunodeficiency (Version 2.37) gene panel.
Sources: Expert list
Created: 1 Apr 2020, 10:11 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
STING-associated vasculopathy, infantile-onset 615934; Type 1 interferonopathies; Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL; Autoinflammatory Disorders

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

Eleanor Williams (Genomics England Curator)

Comment on mode of pathogenicity: In two publications (PMIDs 25029335 and 25401470) the variants have been shown to cause gain of function.
Created: 3 Jul 2018, 1:53 p.m.
Comment on publications: Added publications suggested by reviewer
Created: 3 Jul 2018, 1:51 p.m.
Comment on phenotypes: Added MIM number to STING-associated vasculopathy, infantile-onset
Created: 3 Jul 2018, 1:50 p.m.
In OMIM this gene is associated with STING-associated vasculopathy, infantile-onset. Evidence comes from two publications: Liu et al 2014 (PMID:25029335) and Jeremiah et al 2014 (PMID: 25401470). Liu et al report 6 unrelated patients with STING-associated vasculopathy with onset in infancy in which they identified 3 different de novo heterozygous missense mutations in the TMEM173 gene. The mutation in the first patient was found by whole-exome sequencing, and mutations in the subsequent patients were found by Sanger sequencing. One of the patients was somatic mosaic for the mutation. Studies in patient cells as well as transfection studies in HEK293T cells indicated that the mutations resulted in a gain of function. Jeremiah et al. report 3 affected members of a 3-generation French family of mixed European descent with SAVI identified a heterozygous missense mutation in the STING gene (V155M). In vitro functional expression assays showed that the mutation caused constitutive activation of the IFNB1 promoter, even in the absence of stimulation. More than 3 unrelated cases with plausible disease causing variants.
Created: 3 Jul 2018, 1:50 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

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
Added new-gene-name tag, new approved HGNC gene symbol for TMEM173 is STING1
Created: 6 Sep 2019, 4:14 p.m. | Last Modified: 6 Sep 2019, 4:14 p.m.
Panel Version: 1.54
Comment on list classification: Changed Amber to Green from external review comment and further publications to support gene-disease association
Created: 5 Jul 2018, 2:02 p.m.
Comment on mode of inheritance: updated MOI based on expert review and PMIDs 25029335 and 25401470
Created: 5 Jul 2018, 2:01 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): TMEM173 .PanelApp HGNC gene symbol check: TMEM173 . IUIS Disease: STING--associated vasculopathy, infantile-onset . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL. IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Type 1 Interferonopathies
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: 19 Apr 2018, 12:01 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: STING (TMEM173), PanelApp HGNC gene symbol check: TMEM173, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Type 1 interferonopathies / Type 1 interferonopathies
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: TMEM173, GRID_Gene_Symbol: TMEM173, GRID_Transcript_ENS_Community submitted: ENST00000330794, GRID_Transcript_RefSeq: NM_198282.3, GRID_Transcript_ENS_used_on_Production: ENST00000330794
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • IUIS Classification December 2032
Phenotypes
  • Autoinflammatory Disorders
  • Type 1 interferonopathies
  • Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL
  • STING-associated vasculopathy, infantile-onset 615934
Tags
new-gene-name
OMIM
612374
Clinvar variants
Variants in TMEM173
Penetrance
None
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
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 2032 was added to TMEM173. Mode of inheritance for gene TMEM173 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

1 Apr 2020, Gel status: 3

Set mode of pathogenicity, Set Phenotypes, Set publications

Ellen McDonagh (Genomics England Curator)

Mode of pathogenicity for gene TMEM173 was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Added phenotypes Autoinflammatory Disorders; Type 1 interferonopathies; Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL; STING-associated vasculopathy, infantile-onset 615934 for gene: TMEM173 Publications for gene TMEM173 were updated from 25029335; 25401470; 30705050; 29976662; 29491158; 29425920 to 29425920; 29976662; 29491158; 25029335; 25401470; 30705050

1 Apr 2020, Gel status: 3

Entity classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

Gene: tmem173 has been classified as Green List (High Evidence).

1 Apr 2020, Gel status: 1

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

Ellen McDonagh (Genomics England Curator)

gene: TMEM173 was added gene: TMEM173 was added to Viral susceptibility. Sources: Expert list new-gene-name tags were added to gene: TMEM173. Mode of inheritance for gene: TMEM173 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TMEM173 were set to 25029335; 25401470; 30705050; 29976662; 29491158; 29425920 Phenotypes for gene: TMEM173 were set to STING-associated vasculopathy, infantile-onset 615934; Type 1 interferonopathies; Skin vasculopathy, inflammatory lung disease, systemic autoinflammation and ICC, FCL; Autoinflammatory Disorders