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Primary immunodeficiency or monogenic inflammatory bowel disease v2.529 SLC7A7 Arina Puzriakova Tag for-review was removed from gene: SLC7A7.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.529 SLC7A7 Arina Puzriakova commented on gene: SLC7A7: The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.528 SLC7A7 Arina Puzriakova Source Expert Review Green was added to SLC7A7.
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.481 PI4KA Ivone Leong commented on gene: PI4KA: There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.

Review by Sophie Hambleton (Newcastle University):

"The immunological abnormalities in PI4KA def are obviously rather variable and a slight side-show to the primary GI and neurologic pathology – however that is a detail that should come out when any putative case is reviewed in detail so I would include this as a “CID with associated or syndromic features” on the same basis as TTC7A"
Primary immunodeficiency or monogenic inflammatory bowel disease v2.354 SLC7A7 Arina Puzriakova Classified gene: SLC7A7 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.354 SLC7A7 Arina Puzriakova Gene: slc7a7 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.353 SLC7A7 Arina Puzriakova Tag for-review tag was added to gene: SLC7A7.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.330 TTC7A Eleanor Williams Classified gene: TTC7A as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.330 TTC7A Eleanor Williams Gene: ttc7a has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.209 TTC7A Eleanor Williams Source Other was added to TTC7A.
Publications for gene TTC7A were updated from 24292712; 23423984; 23830146; 24417819; 24417819 to 23423984; 23830146; 24292712; 24417819
Rating Changed from Green List (high evidence) to Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.208 TTC7A Eleanor Williams reviewed gene: TTC7A: Rating: ; Mode of pathogenicity: ; Publications: 24292712, 23423984, 23830146; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.193 SLC7A7 Arina Puzriakova reviewed gene: SLC7A7: Rating: GREEN; Mode of pathogenicity: None; Publications: 32504080; Phenotypes: Lysinuric protein intolerance, 222700; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Classified gene: SLC7A7 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Green. SLC7A7 causes lysinuric protein intolerance (LPI) and immunodeficiency is one of the phenotypes. There are >3 unrelated cases reported on OMIM.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.108 SLC7A7 Ivone Leong Gene: slc7a7 has been classified as Green List (High Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.51 SLC7A7 Zornitza Stark reviewed gene: SLC7A7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Lysinuric protein intolerance, MIM# 222700, Hyper-inflammatory response of macrophages, Normal NK cell function, Lysinuric protein intolerance, Bleeding tendency, Alverolar proteinosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.37 TMEM173 Ellen McDonagh Added comment: Comment on publications: 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/
Primary immunodeficiency or monogenic inflammatory bowel disease v2.36 SLC7A7 Louise Daugherty reviewed gene: SLC7A7: Rating: AMBER; Mode of pathogenicity: ; Publications: 28057010; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v2.35 SLC7A7 Louise Daugherty Publications for gene SLC7A7 were updated from 32086639; 32048120 to 28057010; 32086639; 32048120
Primary immunodeficiency or monogenic inflammatory bowel disease v2.27 SLC7A7 Louise Daugherty Publications for gene: SLC7A7 were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.26 SLC7A7 Louise Daugherty Phenotypes for gene: SLC7A7 were changed from to Lysinuric protein intolerance SLC7A7 deficiency; Severe bacterial infections; Predominantly Antibody Deficiencies; Lysinuric protein intolerance, 222700
Primary immunodeficiency or monogenic inflammatory bowel disease v2.25 SLC7A7 Louise Daugherty Mode of inheritance for gene: SLC7A7 was changed from to BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.15 SLC7A7 Louise Daugherty gene: SLC7A7 was added
gene: SLC7A7 was added to Primary immunodeficiency. Sources: IUIS Classification December 2019
Mode of inheritance for gene: SLC7A7 was set to
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 TTC7A Louise Daugherty commented on gene: TTC7A: 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.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 C7 Louise Daugherty commented on gene: C7: 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.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 TTC7A Louise Daugherty commented on gene: TTC7A: 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.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 C7 Louise Daugherty commented on gene: C7: 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.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 TTC7A Kimberly Gilmour reviewed gene: TTC7A: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 C7 Kimberly Gilmour reviewed gene: C7: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 TTC7A Tracy Briggs reviewed gene: TTC7A: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v1.94 C7 Tracy Briggs reviewed gene: C7: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Primary immunodeficiency or monogenic inflammatory bowel disease v1.60 TTC7A Louise Daugherty Source NHS GMS was added to TTC7A.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.60 C7 Louise Daugherty Source NHS GMS was added to C7.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.59 TTC7A Louise Daugherty Source North West GLH was added to TTC7A.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.59 C7 Louise Daugherty Source North West GLH was added to C7.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.58 TTC7A Louise Daugherty Source London North GLH was added to TTC7A.
Primary immunodeficiency or monogenic inflammatory bowel disease v1.58 C7 Louise Daugherty Source London North GLH was added to C7.
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty commented on gene: TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty commented on gene: C7
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty marked gene: TTC7A as ready
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty classified TTC7A as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty edited their review of gene: TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Sophie Hambleton reviewed gene: TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty marked gene: C7 as ready
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty classified C7 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty edited their review of gene: C7
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Sophie Hambleton reviewed gene: C7
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty commented on C7
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty classified TTC7A as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty commented on TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty commented on TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty commented on C7
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty commented on TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty commented on C7
Primary immunodeficiency or monogenic inflammatory bowel disease TTC7A Louise Daugherty reviewed TTC7A
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty reviewed C7
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty Added gene to panel
Primary immunodeficiency or monogenic inflammatory bowel disease C7 Louise Daugherty Added gene to panel