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COVID-19 research v1.110 TNFAIP3 Arina Puzriakova Phenotypes for gene: TNFAIP3 were changed from A20 deficiency; Autoimmune lymphoproliferative syndrome; Autoinflammatory Disorders; Autoinflammatory syndrome, familial, Behcet-like, 616744; Arthralgia, mucosal ulcers, ocular inflammation to Autoinflammatory syndrome, familial, Behcet-like, OMIM:616744; Autoimmune lymphoproliferative syndrome; Arthralgia, mucosal ulcers, ocular inflammation
COVID-19 research v1.108 TNFRSF1A Arina Puzriakova Phenotypes for gene: TNFRSF1A were changed from Periodic fever, familial 142680; TNF-receptor associated periodic fever syndrome (TRAPS); Recurrent fever, serositis, rash, and ocular or joint inflammation; Autoinflammatory Disorders to Periodic fever, familial, OMIM:142680; TNF-receptor associated periodic fever syndrome (TRAPS); Recurrent fever, serositis, rash, and ocular or joint inflammation; Autoinflammatory Disorders
COVID-19 research v1.56 TNF Sarah Leigh Classified gene: TNF as Green List (high evidence)
COVID-19 research v1.56 TNF Sarah Leigh Added comment: Comment on list classification: Various publications demonstrating associations between TNF variants and viral infection susceptibility and progression.
COVID-19 research v1.56 TNF Sarah Leigh Gene: tnf has been classified as Green List (High Evidence).
COVID-19 research v1.55 TNF Sarah Leigh Mode of inheritance for gene: TNF was changed from to Unknown
COVID-19 research v1.52 IFNG Sarah Leigh changed review comment from: IFNG was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility). "Illumina review: From OMIM: Interferon-gamma (IFNG), or type II interferon, is a cytokine critical for innate and adaptive immunity against viral and intracellular bacterial infections and for tumor control. The importance of IFNG in the immune system stems in part from its ability to inhibit viral replication directly, but most importantly derives from its immunostimulatory and immunomodulatory effects. IFNG is produced predominantly by natural killer (NK) and natural killer T (NKT) cells as part of the innate immune response, and by CD4 (186940) and CD8 (see 186910) cytotoxic T lymphocyte (CTL) effector T cells once antigen-specific immunity develops (PMID: 178981204; Schoenborn and Wilson, 2007). From OMIM: PMID: 17215375: Huang et al. (2007) The IFNG gene SNP, -764 C>G (rs2069707) in the proximal promoter region next to the binding motif for HSF1 , was significantly associated with sustained virologic response to IFNA therapy in a cohort of hepatitis C virus-positive patients compared to a cohorts who had spontaneously cleared HCV infection or who had chronic HCV infection. Luciferase reporter and EMSA analyses showed that the -764G allele had 2- to 3-fold higher promoter activity and stronger binding affinity for HSF1 than the -764C allele. Huang et al. (2007) concluded that the -764C-G SNP is functionally important in determining viral clearance and treatment response in HCV-infected patients.
From OMIM PMID: 12854077: An et al. (2003) reported an association between a SNP in the IFNG promoter region, -173 G>T, and progression to AIDS. In individuals with the rare -179T allele, but not in those with the -179G allele, IFNG is inducible by TNF. An et al. (2003) studied 298 African American HIV-1 seroconverters and found that the -179T allele was associated with accelerated progression to a CD4 cell count below 200 and to AIDS. They noted that the SNP is present in 4% of African Americans and in only 0.02% of European Americans.
PMID: 26458193 Wei et al. (2017) Eleven independent case-control studies were selected for the meta-analysis, comprising a total of 1527 HBV cases and 1467 healthy subjects. carriers of the IFN-γ A allele were more likely to develop HBV infection than those without in all five genetic models (all p < 0.05). According to the ethnicity-based sub-group analysis, a significant difference of the IFN-γ rs2430561 T > A (IFN-γ +874T/A) polymorphism was detected associated with the increased risk of HBV infection in Asians and European-derived populations in the majority of the groups.
; to: IFNG was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility). Illumina review: From OMIM: Interferon-gamma (IFNG), or type II interferon, is a cytokine critical for innate and adaptive immunity against viral and intracellular bacterial infections and for tumor control. The importance of IFNG in the immune system stems in part from its ability to inhibit viral replication directly, but most importantly derives from its immunostimulatory and immunomodulatory effects. IFNG is produced predominantly by natural killer (NK) and natural killer T (NKT) cells as part of the innate immune response, and by CD4 (186940) and CD8 (see 186910) cytotoxic T lymphocyte (CTL) effector T cells once antigen-specific immunity develops (PMID: 17981204; Schoenborn and Wilson, 2007). From OMIM: PMID: 17215375: Huang et al. (2007) The IFNG gene SNP, -764 C>G (rs2069707) in the proximal promoter region next to the binding motif for HSF1 , was significantly associated with sustained virologic response to IFNA therapy in a cohort of hepatitis C virus-positive patients compared to a cohorts who had spontaneously cleared HCV infection or who had chronic HCV infection. Luciferase reporter and EMSA analyses showed that the -764G allele had 2- to 3-fold higher promoter activity and stronger binding affinity for HSF1 than the -764C allele. Huang et al. (2007) concluded that the -764C-G SNP is functionally important in determining viral clearance and treatment response in HCV-infected patients.
From OMIM PMID: 12854077: An et al. (2003) reported an association between a SNP in the IFNG promoter region, -173 G>T, and progression to AIDS. In individuals with the rare -179T allele, but not in those with the -179G allele, IFNG is inducible by TNF. An et al. (2003) studied 298 African American HIV-1 seroconverters and found that the -179T allele was associated with accelerated progression to a CD4 cell count below 200 and to AIDS. They noted that the SNP is present in 4% of African Americans and in only 0.02% of European Americans.
PMID: 26458193 Wei et al. (2017) Eleven independent case-control studies were selected for the meta-analysis, comprising a total of 1527 HBV cases and 1467 healthy subjects. carriers of the IFN-γ A allele were more likely to develop HBV infection than those without in all five genetic models (all p < 0.05). According to the ethnicity-based sub-group analysis, a significant difference of the IFN-γ rs2430561 T > A (IFN-γ +874T/A) polymorphism was detected associated with the increased risk of HBV infection in Asians and European-derived populations in the majority of the groups.
COVID-19 research v1.38 TNF Sarah Leigh changed review comment from: TNF was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility); to: TNF was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility). Illumina review: PMID: 10719836: Herbein et al. (Review) TNF is a proinflammatory cytokine plays a key role in the host response to viral infection. TNF enhances or inhibits viral replication depending on the virus involved and the cell type infected. The binding of TNF to the TNF receptors can activate, differentiate, or kill target cells thereby interfering with the viral life cycle. In contrast, viruses have evolved to appropriate the TNF/TNFR pathway to evade immune responses and favor viral dissemination. From OMIM: PMID: 12915457;Kim et al. (2003) To investigate whether TNF-alpha promoter polymorphisms are associated with clearance of hepatitis B virus (HBV) infection, Kim et al. (2003) genotyped 1,400 Korean subjects, 1,109 of whom were chronic HBV carriers and 291 who spontaneously recovered. The TNF promoter alleles that were previously reported to be associated with higher plasma levels (presence of -308A or the absence of -863A alleles), were strongly associated with the resolution of HBV infection. Haplotype analysis revealed that TNF-alpha haplotype 1 (-1031T; -863C; -857C; -308G; -238G; -163G) and haplotype 2 (-1031C; -863A; -857C; -308G; -238G; -163G) were significantly associated with HBV clearance, showing protective antibody production and persistent HBV infection, respectively (P = 0.003-0.02). From OMIM: PMID: 11506397 Quasney et al. The presence of the A allele at the TNF-alpha-308 site was overrepresented among adults with HIV dementia compared to those without dementia (0.28 vs 0.07; OR 5.5; 95% CI 1.8-17.0) and a healthy control population (0.28 vs 0.11). The increased frequency of the A allele in HlV-infected adults with dementia suggests that this locus may play a role in the pathophysiology of dementia and suggests a genetic predisposition for the development of HIV dementia. PMID: 26657940 García-Ramírez et al. (2015) - 145 patients with influenza A (H1N1) (pA/H1N1), 133 patients with influenza-like illness (ILI), and 360 asymptomatic healthy contacts (AHCs) were included from a Mexican population were studied. The TNF-238 GA genotype was associated with an increased risk of disease severity (OR =16.06, p = 0.007). PMID: 31986264: Huang et al. (2020) Study of 41 patients admitted to hospital with laboratory-confirmed 2019-nCoV. Compared with non-ICU patients, ICU patients had higher plasma levels of proinflammatory cytokines and chemokines including IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα.
COVID-19 research v1.38 TNF Sarah Leigh Publications for gene: TNF were set to
COVID-19 research v1.30 IFNG Sarah Leigh changed review comment from: IFNG was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility); to: IFNG was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility). "Illumina review: From OMIM: Interferon-gamma (IFNG), or type II interferon, is a cytokine critical for innate and adaptive immunity against viral and intracellular bacterial infections and for tumor control. The importance of IFNG in the immune system stems in part from its ability to inhibit viral replication directly, but most importantly derives from its immunostimulatory and immunomodulatory effects. IFNG is produced predominantly by natural killer (NK) and natural killer T (NKT) cells as part of the innate immune response, and by CD4 (186940) and CD8 (see 186910) cytotoxic T lymphocyte (CTL) effector T cells once antigen-specific immunity develops (PMID: 178981204; Schoenborn and Wilson, 2007). From OMIM: PMID: 17215375: Huang et al. (2007) The IFNG gene SNP, -764 C>G (rs2069707) in the proximal promoter region next to the binding motif for HSF1 , was significantly associated with sustained virologic response to IFNA therapy in a cohort of hepatitis C virus-positive patients compared to a cohorts who had spontaneously cleared HCV infection or who had chronic HCV infection. Luciferase reporter and EMSA analyses showed that the -764G allele had 2- to 3-fold higher promoter activity and stronger binding affinity for HSF1 than the -764C allele. Huang et al. (2007) concluded that the -764C-G SNP is functionally important in determining viral clearance and treatment response in HCV-infected patients.
From OMIM PMID: 12854077: An et al. (2003) reported an association between a SNP in the IFNG promoter region, -173 G>T, and progression to AIDS. In individuals with the rare -179T allele, but not in those with the -179G allele, IFNG is inducible by TNF. An et al. (2003) studied 298 African American HIV-1 seroconverters and found that the -179T allele was associated with accelerated progression to a CD4 cell count below 200 and to AIDS. They noted that the SNP is present in 4% of African Americans and in only 0.02% of European Americans.
PMID: 26458193 Wei et al. (2017) Eleven independent case-control studies were selected for the meta-analysis, comprising a total of 1527 HBV cases and 1467 healthy subjects. carriers of the IFN-γ A allele were more likely to develop HBV infection than those without in all five genetic models (all p < 0.05). According to the ethnicity-based sub-group analysis, a significant difference of the IFN-γ rs2430561 T > A (IFN-γ +874T/A) polymorphism was detected associated with the increased risk of HBV infection in Asians and European-derived populations in the majority of the groups.
COVID-19 research v1.11 TNF Alison Coffey reviewed gene: TNF: Rating: GREEN; Mode of pathogenicity: ; Publications: 10719836, 12915457, 11506397, 26657940, 31986264; Phenotypes: ; Mode of inheritance: Unknown
COVID-19 research v1.10 TNF Sarah Leigh commented on gene: TNF: TNF was identified through an OMIM search for potential viral susceptibility genes. Initial triage by Illumina (Alison Coffey and team) was given a Tier 3 grouping (experimental evidence and association data consistent with viral susceptibility)
COVID-19 research v0.371 TNFSF10 Rebecca Foulger Classified gene: TNFSF10 as Amber List (moderate evidence)
COVID-19 research v0.371 TNFSF10 Rebecca Foulger Added comment: Comment on list classification: Kept the Amber rating initially suggested by Illumina curation team: plays a role in viral surveillance, and virus can modulate TNFSF10 (TRAIL) signaling. Many studies look at expression levels following infection. No direct susceptibility studies, so Amber appropriate.
COVID-19 research v0.371 TNFSF10 Rebecca Foulger Gene: tnfsf10 has been classified as Amber List (Moderate Evidence).
COVID-19 research v0.370 TNFSF10 Rebecca Foulger Publications for gene: TNFSF10 were set to 18802095; 14702109; 31725732; 27740879; 17913827; 15110181
COVID-19 research v0.369 TNFSF10 Rebecca Foulger changed review comment from: Summary of literature: TNFSF10/TRAIL is a death ligand that contributes to immune surveillance against virus-infected cells via the death receptor TNFRSF10B/DR5. TNFSF10 binding induces the caspase cascade to kill the virus-infected cell. Many viruses evade antiviral immunity by modulating TNFSF10 receptor signaling.; to: Summary of literature: TNFSF10/TRAIL is a death ligand that contributes to immune surveillance against virus-infected cells via the death receptor DR5. TNFSF10 binding induces the caspase cascade to kill the virus-infected cell. Many viruses evade antiviral immunity by modulating TNFSF10 receptor signaling.
COVID-19 research v0.369 TNFSF10 Rebecca Foulger commented on gene: TNFSF10: Summary of literature: TNFSF10/TRAIL is a death ligand that contributes to immune surveillance against virus-infected cells via the death receptor TNFRSF10B/DR5. TNFSF10 binding induces the caspase cascade to kill the virus-infected cell. Many viruses evade antiviral immunity by modulating TNFSF10 receptor signaling.
COVID-19 research v0.368 TNFSF10 Rebecca Foulger Publications for gene: TNFSF10 were set to 18802095; 14702109
COVID-19 research v0.365 TNFSF4 Sarah Leigh changed review comment from: TNFSF4 was identified through an OMIM search for potential viral susceptibility genes. Based on initial triage by Illumina (Tier 5 grouping).
Tumor necrosis factor (TNF) family cytokines function as prominent mediators of immune regulation and the inflammatory response. Most TNF family cytokines are expressed as type II transmembrane proteins, with homology confined to approximately 150 C-terminal residues. The TNF ligands interact with a parallel family of receptors (reviewed by Alison Coffey and team, Illumina).
TNFSF4 is a cell surface glycoprotein antigen that is expressed in T-cell leukemia virus type 1 (HTLV-1) infected human cells (PMID 7913952;8076595). Functional analysis showed that anti-TNFSF4 monoclonal antibody inhibited T-cell proliferation (PMID 11359859).; to: TNFSF4 was identified through an OMIM search for potential viral susceptibility genes. Based on initial triage by Illumina (Tier 5 grouping).
Tumor necrosis factor (TNF) family cytokines function as prominent mediators of immune regulation and the inflammatory response. Most TNF family cytokines are expressed as type II transmembrane proteins, with homology confined to approximately 150 C-terminal residues. The TNF ligands interact with a parallel family of receptors (reviewed by Alison Coffey and team, Illumina).
TNFSF4 is a cell surface glycoprotein antigen that is expressed in T-cell leukemia virus type 1 (HTLV-1) infected human cells (PMID 7913952;8076595). Functional analysis showed that anti-TNFSF4 monoclonal antibody inhibited T-cell proliferation (PMID 11359859).
PMID 31725732: suggests that TNFSF4, one of the major causative cytokine factors in African swine fever virus pathogenesis, via inducing apoptosis.
COVID-19 research v0.365 TNFSF4 Sarah Leigh Publications for gene: TNFSF4 were set to 7913952; 8076595; 11359859
COVID-19 research v0.362 TNFSF4 Sarah Leigh Classified gene: TNFSF4 as Red List (low evidence)
COVID-19 research v0.362 TNFSF4 Sarah Leigh Gene: tnfsf4 has been classified as Red List (Low Evidence).
COVID-19 research v0.361 TNFSF4 Sarah Leigh commented on gene: TNFSF4
COVID-19 research v0.361 TNFSF4 Sarah Leigh Publications for gene: TNFSF4 were set to 7913952; 8076595
COVID-19 research v0.360 TNFSF4 Sarah Leigh Publications for gene: TNFSF4 were set to
COVID-19 research v0.359 TNFSF10 Rebecca Foulger Publications for gene: TNFSF10 were set to
COVID-19 research v0.348 KLF2 Rebecca Foulger commented on gene: KLF2: Evidence Summary from Illumina curation team (Alison Coffey and Julie Taylor): KLF2 is a member of the Kruppel-like factor (KLF) family of zinc finger transcription factors that function in cell differentiation, quiescence, and homeostasis. It also plays a regulatory role in inflammation-related pathways (Jha and Das 2017). Richardson et al. (2012) showed that KLF2 acts as a host factor that modulates CCR5 expression in CD4 T cells and influences susceptibility to infection with CCR5-dependent HIV-1 strains. Huang et al. (2017) showed through both network analyses and experimental results that KLF2 plays a central role in regulating many genes associated with acute respiratory distress syndrome (ARDS) identified by GWAS and that overexpression of KLF2 in vivo in mice could mitigate lung injury and expression of inflammatory genes, including that induced by influenza A virus.

PMID 17141159: Lee et al. (2006) - KLF2 deficient mice die in prenatal stage due to vascular defects, highlighting its crucial role in embryonic development. Lethal high-output heart failure, as found in the KO mice, was also observed in zebrafish embryos after morpholino inhibition of the Klf2 ortholog klf2a. CD4+ T cells from KLF2-deficient mice expressed multiple inflammatory chemokine receptors, suggesting that loss of KLF2 leads to redirection of naïve T cells to nonlymphoid sites (Sebzda et al., 2008).

PMID 19592277: Weinreich et al. (2009) - Demonstrated upregulation of the chemokine receptor CXCR3 on KLF2-deficient T cells (Fig. 1). KLF2-deficient T cells also overproduced IL-4 (Fig. 5).

PMID 22988032: Richardson et al. (2012) - Tested whether the abundance of KLF2 after T cell activation regulates CCR5 expression and, thus, susceptibility of a T cell to CCR5-dependent HIV-1 strains (R5). Introduced small interfering RNA targeting KLF2 expression and demonstrated that reduced KLF2 expression also resulted in less CCR5 (Fig. 3). Introduction of KLF2 under control of a heterologous promoter could restore CCR5 expression and R5 susceptibility to CD3/28 costimulated T cells and some transformed cell lines (Fig. 5, 6). KLF2 is a host factor that modulates CCR5 expression in CD4 T cells and influences susceptibility to R5 infection.

PMID 29125549: (review) Jha and Das (2017) - KLF2 also plays a critical regulatory role in various inflammatory diseases and their pathogenesis.

PMID 27855271: Huang et al. (2017) - Animal and in vitro models of acute lung injury were used to characterize KLF2 expression and its downstream effects responding to influenza A virus (A/WSN/33 [H1N1]), tumor necrosis factor-α, LPS, mechanical stretch/ventilation, or microvascular flow to examine the role of the gene in endothelial barrier disruption and cytokine storm in experimental lung injury. Pulmonary Klf2 was down-regulated by inflammation induced by influenza A/WSN/H1N1 virus (H1N1) infection, LPS administration, or LPS administration followed by high tidal volume ventilation in vivo (Fig. 1). It was also down-regulated by pathologic stretch and inflammatory stimuli (Fig. 2). Knockdown of endogenous KLF2 reduces Rac1 activation in human pulmonary microvascular cells, whereas adenovirus-mediated transduction with KLF2 promoted Rac1 activation (Fig. 3). Computational predictive pathway analysis suggested that KLF2 acts to regulate ARDS-associated GWAS genes, including ACE, NAD(P)H, NQO1, SERPINE1/PAI-1, TNF, and NF-kappaB. Expression studies in mice confirmed this regulatory role (Fig. 8). Overexpression of KLF2 in vivo in mice could also mitigate lung injury and expression of inflammatory genes (Fig. 7).
COVID-19 research v0.347 CXADR Alison Coffey commented on gene: CXADR: Evidence Summary from Illumina curation team: The coxsackie and adenovirus receptor (CXADR or CAR), also known as CAR-like membrane protein (CLMP), was first identified as a high affinity receptor for adenovirus serotypes 2 and 5 and coxsackie viruses group B. CXADR is developmentally regulated and plays an important role in cardiac development. The protein is a transmembrane receptor and plays a key role in controlling adhesion between adjacent epithelial cells. It is also implicated in controlling both recruitment of immune cells and in tumorigenesis (Zapater et al. 2017). Vehik et al. (2018) concluded that a SNP within the CXADR region is associated with islet autoimmunity. In response to exogenous TNF?, CAR promotes transmigration of leukocytes both in vitro and in vivo. suggesting that CAR may be an important receptor in the control of inflammation. As neutrophils and T cells play a role in host immunity, these data suggest that CAR may be ideally positioned to modulate the immune response from the epithelial or endothelial cell compartments. (Morton et al 2016). CAR expression and infectivity with adenovirus (Ad) are increased in cystic fibrosis airway epithelial cells (Sharma et al. 2017).
COVID-19 research v0.338 TNFSF4 Sarah Leigh gene: TNFSF4 was added
gene: TNFSF4 was added to COVID-19 research. Sources: OMIM
Mode of inheritance for gene: TNFSF4 was set to Unknown
Phenotypes for gene: TNFSF4 were set to {Myocardial infarction, susceptibility to} 608446
COVID-19 research v0.336 TNFSF10 Rebecca Foulger commented on gene: TNFSF10
COVID-19 research v0.333 TNFSF10 Rebecca Foulger gene: TNFSF10 was added
gene: TNFSF10 was added to COVID-19 research. Sources: Expert list,OMIM,Expert Review Amber
Mode of inheritance for gene: TNFSF10 was set to Unknown
COVID-19 research v0.262 HIVEP1 Rebecca Foulger Added comment: Comment on publications: Note that PMID:24719322 (Modulation of TLR3, TLR4 and TLR7 Mediated IFN-β, Rantes and TNFα Production by HIVEP1) was withdrawn by the author.
COVID-19 research v0.203 TNFSF11 Sophie Hambleton reviewed gene: TNFSF11: Rating: GREEN; Mode of pathogenicity: None; Publications: 17632511; Phenotypes: osteopetrosis, osteoclast-poor; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.203 TNFRSF9 Sophie Hambleton reviewed gene: TNFRSF9: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: immunodeficiency, autoimmunity, lymphoma, EBV predisposition; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
COVID-19 research v0.176 TNF Sarah Leigh reviewed gene: TNF: Rating: RED; Mode of pathogenicity: ; Publications: 12915457; Phenotypes: ; Mode of inheritance:
COVID-19 research v0.121 TNF Sarah Leigh gene: TNF was added
gene: TNF was added to Viral susceptibility. Sources: OMIM
Mode of inheritance for gene: TNF was set to
COVID-19 research v0.40 TNFSF12 Ellen McDonagh Source Expert Review Green was added to TNFSF12.
Added phenotypes Immunodeficiency, common variable with lack of anti-pneumococcal antibody; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia; Pneumonia, bacterial infections, warts, thrombocytopenia for gene: TNFSF12
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF13B Ellen McDonagh Source Expert Review Green was added to TNFRSF13B.
Added phenotypes IgA with IgG subclass deficiency; Immunodeficiency, common variable, 2; Immunodeficiency, common variable, 2, 240500; Variable clinical expression; Isolated IgG subclass deficiency; IGAD; Selective IgA deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Immunoglobulin A deficiency 2, 609529; CVID for gene: TNFRSF13B
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFSF11 Ellen McDonagh Source Expert Review Green was added to TNFSF11.
Added phenotypes Osteopetrosis with severe growth retardation; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: TNFSF11
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF9 Ellen McDonagh Source Expert Review Green was added to TNFRSF9.
Added phenotypes EBV lymphoproliferation, B-cell lymphoma; CD137 deficiency (41BB) for gene: TNFRSF9
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF4 Ellen McDonagh Source Expert Review Green was added to TNFRSF4.
Added phenotypes Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency; Immunodeficiencies affecting cellular and humoral immunity; Impaired immunity to HHV8, Kaposis sarcoma; Combined immunodeficiency for gene: TNFRSF4
Rating Changed from Red List (low evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF13C Ellen McDonagh Source Expert Review Green was added to TNFRSF13C.
Added phenotypes Immunodeficiency, common variable, 4; Variable clinical expression; Isolated IgG subclass deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies for gene: TNFRSF13C
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.40 TNFRSF11A Ellen McDonagh Source Expert Review Green was added to TNFRSF11A.
Added phenotypes Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity for gene: TNFRSF11A
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
COVID-19 research v0.36 TNFSF12 Ellen McDonagh gene: TNFSF12 was added
gene: TNFSF12 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFSF12 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFSF12 were set to 23493554; 32086639; 32048120
Phenotypes for gene: TNFSF12 were set to Immunodeficiency, common variable with lack of anti-pneumococcal antibody; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia; Pneumonia, bacterial infections, warts, thrombocytopenia
COVID-19 research v0.36 TNFRSF1A Ellen McDonagh gene: TNFRSF1A was added
gene: TNFRSF1A was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF1A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFRSF1A were set to 11175303; 10199409; 10902757; 17360963
Phenotypes for gene: TNFRSF1A were set to Periodic fever, familial 142680; TNF-receptor associated periodic fever syndrome (TRAPS); Recurrent fever, serositis, rash, and ocular or joint inflammation; Autoinflammatory Disorders
COVID-19 research v0.36 TNFAIP3 Ellen McDonagh gene: TNFAIP3 was added
gene: TNFAIP3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,NHS GMS,London North GLH,IUIS Classification February 2018
Mode of inheritance for gene: TNFAIP3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNFAIP3 were set to 27845235; 29572183; 26642243; 28659290; 29317407
Phenotypes for gene: TNFAIP3 were set to A20 deficiency; Autoimmune lymphoproliferative syndrome; Autoinflammatory Disorders; Autoinflammatory syndrome, familial, Behcet-like, 616744; Arthralgia, mucosal ulcers, ocular inflammation
COVID-19 research v0.36 TNFRSF13B Ellen McDonagh gene: TNFRSF13B was added
gene: TNFRSF13B was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,IUIS Classification December 2019,GRID V2.0,GOSH PID v.8.0,A- or hypo-gammaglobulinaemia v1.25,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF13B was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: TNFRSF13B were set to 29114388; 28834165; 16007086; 16007087; 32086639; 18981294; 32048120
Phenotypes for gene: TNFRSF13B were set to IgA with IgG subclass deficiency; Immunodeficiency, common variable, 2; Immunodeficiency, common variable, 2, 240500; Variable clinical expression; Isolated IgG subclass deficiency; IGAD; Selective IgA deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies; Immunoglobulin A deficiency 2, 609529; CVID
COVID-19 research v0.36 TNFSF11 Ellen McDonagh gene: TNFSF11 was added
gene: TNFSF11 was added to Viral susceptibility. Sources: IUIS Classification February 2018,IUIS Classification December 2019
Mode of inheritance for gene: TNFSF11 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFSF11 were set to 32086639; 32048120
Phenotypes for gene: TNFSF11 were set to Osteopetrosis with severe growth retardation; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity
COVID-19 research v0.36 TNFRSF9 Ellen McDonagh gene: TNFRSF9 was added
gene: TNFRSF9 was added to Viral susceptibility. Sources: IUIS Classification December 2019
Mode of inheritance for gene: TNFRSF9 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF9 were set to 30872117; 32086639; 31537641; 31501153; 32048120
Phenotypes for gene: TNFRSF9 were set to EBV lymphoproliferation, B-cell lymphoma; CD137 deficiency (41BB)
COVID-19 research v0.36 TNFRSF4 Ellen McDonagh gene: TNFRSF4 was added
gene: TNFRSF4 was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018
Mode of inheritance for gene: TNFRSF4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF4 were set to 32086639; 32048120
Phenotypes for gene: TNFRSF4 were set to Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency; Immunodeficiencies affecting cellular and humoral immunity; Impaired immunity to HHV8, Kaposis sarcoma; Combined immunodeficiency
COVID-19 research v0.36 TNFRSF13C Ellen McDonagh gene: TNFRSF13C was added
gene: TNFRSF13C was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TNFRSF13C was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF13C were set to 32086639; 32048120
Phenotypes for gene: TNFRSF13C were set to Immunodeficiency, common variable, 4; Variable clinical expression; Isolated IgG subclass deficiency; Common variable immunodeficiency disorders (CVID); Predominantly Antibody Deficiencies
COVID-19 research v0.36 TNFRSF11A Ellen McDonagh gene: TNFRSF11A was added
gene: TNFRSF11A was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber
Mode of inheritance for gene: TNFRSF11A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TNFRSF11A were set to 32086639; 32048120
Phenotypes for gene: TNFRSF11A were set to Osteopetrosis; Defects in intrinsic and innate immunity; Defects in Intrinsic and Innate Immunity