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| COVID-19 research v1.129 | TTC37 | Sarah Leigh changed review comment from: The new_gene_name tag has been added. The new name for TTC37 is SKIC3.; to: Added new-gene-name tag, new approved HGNC gene symbol for TTC37 is SKIC3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v1.129 | TTC37 | Sarah Leigh Tag new-gene-name tag was added to gene: TTC37. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v1.129 | TTC37 | Sarah Leigh commented on gene: TTC37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v1.128 | SLC37A4 | Arina Puzriakova Phenotypes for gene: SLC37A4 were changed from Glycogen storage disease Ib; Congenital defects of phagocyte number or function; Glycogen storage disease Ib, 232220; Glycogen storage disease type 1b (GS1b); Glycogen storage disease with or without neutropenia; Glycogen storage disease Ic; Fasting hypoglycemia, lactic acidosis, hyperlipidemia, hepatomegaly to Glycogen storage disease Ib, OMIM:232220; Glycogen storage disease Ic, OMIM:232240; Fasting hypoglycemia, lactic acidosis, hyperlipidemia, hepatomegaly; Congenital defects of phagocyte number or function | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.334 | ABCB1 |
Ivone Leong Added comment: Comment on publications: PMID: 18547906 showed that ABCB1 SNP (C3435T) is associated with virological efficacy in treatments for HIV infected pateints. PMID: 26922556 showed that SNPS in ABCB1 may influence HCV infectivity. |
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| COVID-19 research v0.315 | ZC3HC1 | Sarah Leigh commented on gene: ZC3HC1: One of the 25 top novel PID-associated genes in a large-cohort WGS analysis, using BeviMed assessment of enrichment for candidate disease-causing variants in individual genes (https://doi.org/10.1101/499988). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.311 | SERINC5 |
Catherine Snow changed review comment from: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". Currently no gene disease association for SERINC5 Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3 inhibited infectivity of human immunodeficiency virus (HIV)-1 and murine leukemia retrovirus (MLV) Sudderuddin et al (2020) found that SERINC5 on the cell surface is down regulated upon HIV infection Sources: Literature; to: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". Currently no gene disease association for SERINC5. Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3 inhibited infectivity of human immunodeficiency virus (HIV)-1 and murine leukemia retrovirus (MLV) Sudderuddin et al (2020) found that SERINC5 on the cell surface is down regulated upon HIV infection Sources: Literature |
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| COVID-19 research v0.310 | SERINC5 |
Catherine Snow gene: SERINC5 was added gene: SERINC5 was added to COVID-19 research. Sources: Literature Mode of inheritance for gene: SERINC5 was set to Unknown Publications for gene: SERINC5 were set to 26416734; 31918727 Review for gene: SERINC5 was set to AMBER Added comment: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". Currently no gene disease association for SERINC5 Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3 inhibited infectivity of human immunodeficiency virus (HIV)-1 and murine leukemia retrovirus (MLV) Sudderuddin et al (2020) found that SERINC5 on the cell surface is down regulated upon HIV infection Sources: Literature |
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| COVID-19 research v0.309 | SERINC3 | Catherine Snow Publications for gene: SERINC3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.308 | SERINC3 |
Catherine Snow changed review comment from: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". No current gene disease relationship in OMIM. The human immunodeficiency virus (HIV)-1 Nef protein and the unrelated murine leukemia virus (MLV) glycosylated Gag (glycoGag) protein enhance HIV-1 infectivity. Usami et al. (2015) found that silencing both SERINC3 and SERINC5 (614551) precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. CD4-positive T cells lacking both SERINC3 and SERINC5 showed significantly increased susceptibility to Nef-deficient virions. SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. Usami et al. (2015) proposed that inhibiting Nef-mediated downregulation of SERINC3 and SERINC5, which are normally highly expressed in HIV-1 target cells, has the potential to combat HIV/AIDS. Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3 (607165), inhibited infectivity of human immunodeficiency virus (HIV)-1 (see 609423) and murine leukemia retrovirus (MLV) Sources: Literature; to: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". No current gene disease relationship in OMIM. The human immunodeficiency virus (HIV)-1 Nef protein and the unrelated murine leukemia virus (MLV) glycosylated Gag (glycoGag) protein enhance HIV-1 infectivity. Usami et al. (2015) found that silencing both SERINC3 and SERINC5 (614551) precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. CD4-positive T cells lacking both SERINC3 and SERINC5 showed significantly increased susceptibility to Nef-deficient virions. SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. Usami et al. (2015) proposed that inhibiting Nef-mediated downregulation of SERINC3 and SERINC5, which are normally highly expressed in HIV-1 target cells, has the potential to combat HIV/AIDS. Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3, inhibited infectivity of human immunodeficiency virus (HIV)-1 and murine leukemia retrovirus (MLV) Sources: Literature |
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| COVID-19 research v0.308 | SERINC3 | Catherine Snow Classified gene: SERINC3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.308 | SERINC3 | Catherine Snow Gene: serinc3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.307 | SERINC3 |
Catherine Snow changed review comment from: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". No current gene disease relationship in OMIM. The human immunodeficiency virus (HIV)-1 Nef protein and the unrelated murine leukemia virus (MLV) glycosylated Gag (glycoGag) protein enhance HIV-1 infectivity. Usami et al. (2015) found that silencing both SERINC3 and SERINC5 (614551) precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. CD4-positive T cells lacking both SERINC3 and SERINC5 showed significantly increased susceptibility to Nef-deficient virions. SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. Usami et al. (2015) proposed that inhibiting Nef-mediated downregulation of SERINC3 and SERINC5, which are normally highly expressed in HIV-1 target cells, has the potential to combat HIV/AIDS. Sources: Literature; to: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". No current gene disease relationship in OMIM. The human immunodeficiency virus (HIV)-1 Nef protein and the unrelated murine leukemia virus (MLV) glycosylated Gag (glycoGag) protein enhance HIV-1 infectivity. Usami et al. (2015) found that silencing both SERINC3 and SERINC5 (614551) precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. CD4-positive T cells lacking both SERINC3 and SERINC5 showed significantly increased susceptibility to Nef-deficient virions. SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. Usami et al. (2015) proposed that inhibiting Nef-mediated downregulation of SERINC3 and SERINC5, which are normally highly expressed in HIV-1 target cells, has the potential to combat HIV/AIDS. Screening human cell lines and using CRISPR-Cas9 analysis, Rosa et al. (2015) found that SERINC5, and to a lesser extent SERINC3 (607165), inhibited infectivity of human immunodeficiency virus (HIV)-1 (see 609423) and murine leukemia retrovirus (MLV) Sources: Literature |
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| COVID-19 research v0.307 | SERINC3 |
Catherine Snow gene: SERINC3 was added gene: SERINC3 was added to COVID-19 research. Sources: Literature Mode of inheritance for gene: SERINC3 was set to Unknown Review for gene: SERINC3 was set to AMBER Added comment: Curation by Illumina clinical curators contributing to Covid-19 effort. Curation on all OMIM genes which hit the term "virus". No current gene disease relationship in OMIM. The human immunodeficiency virus (HIV)-1 Nef protein and the unrelated murine leukemia virus (MLV) glycosylated Gag (glycoGag) protein enhance HIV-1 infectivity. Usami et al. (2015) found that silencing both SERINC3 and SERINC5 (614551) precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. CD4-positive T cells lacking both SERINC3 and SERINC5 showed significantly increased susceptibility to Nef-deficient virions. SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. Usami et al. (2015) proposed that inhibiting Nef-mediated downregulation of SERINC3 and SERINC5, which are normally highly expressed in HIV-1 target cells, has the potential to combat HIV/AIDS. Sources: Literature |
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| COVID-19 research v0.260 | ZC3HC1 | Sarah Leigh reviewed gene: ZC3HC1: Rating: RED; Mode of pathogenicity: ; Publications: https://doi.org/10.1101/499988; Phenotypes: primary immunodeficiency; Mode of inheritance: Unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.257 | ZC3HC1 |
Sarah Leigh gene: ZC3HC1 was added gene: ZC3HC1 was added to COVID-19 research. Sources: Literature Mode of inheritance for gene: ZC3HC1 was set to Unknown |
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| COVID-19 research v0.180 | SLC39A7 | Sophie Hambleton reviewed gene: SLC39A7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: agammaglobulinaemia, B cell deficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.139 | LY6E |
Eleanor Williams gene: LY6E was added gene: LY6E was added to Viral susceptibility. Sources: Literature Mode of inheritance for gene: LY6E was set to Unknown Review for gene: LY6E was set to RED Added comment: Preprint - https://www.biorxiv.org/content/10.1101/2020.04.02.021469v1 - Zhao et al Found that human cell line C3A was more susceptible to human coronavirus HCoV-OC43 infection than HepG2. Ectopic expression of LY6E in HEK 293 cells inhibited the entry of HCoV-OC43. Overexpression of LY6E in C3A and A549 cells efficiently inhibited the infection of HCoV-OC43 and knockdown of LY6E expression in HepG2 significantly increased its susceptibility to HCoV-OC43 infection. LY6E also restricted the entry mediated by the envelope spike proteins of other human coronaviruses, including the currently pandemic SARS-CoV-2. Sources: Literature |
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| COVID-19 research v0.108 | RECQL4 | Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 5 variants reported in 3 unrelated cases in which immunodeficiecy was a feature (PMID 16630167; 21143835; 26064716). In addition RECQL4 variants have been implicated in Acrodermatitis Enteropathica caused by SLC39A4 (p.Gly512Trp)(PMID 30174688) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.103 | C3 | Ivone Leong reviewed gene: C3: Rating: GREEN; Mode of pathogenicity: ; Publications: 32086639, 32048120; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.102 | C3 |
Ivone Leong Source IUIS Classification December 2022 was added to C3. Mode of inheritance for gene C3 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| COVID-19 research v0.93 | RC3H1 | Sarah Leigh Classified gene: RC3H1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.93 | RC3H1 | Sarah Leigh Gene: rc3h1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.92 | RC3H1 | Sarah Leigh Publications for gene: RC3H1 were set to PMID: 31636267 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| COVID-19 research v0.40 | SLC39A7 |
Ellen McDonagh Source Expert Review Green was added to SLC39A7. Added phenotypes Agammaglobulinemia; B cell deficiency; Early onset infections, blistering dermatosis, failure to thrive, thrombocytopenia; Predominantly Antibody Deficiencies for gene: SLC39A7 Rating Changed from Red List (low evidence) to Green List (high evidence) |
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| COVID-19 research v0.40 | RAC2 |
Ellen McDonagh Source Expert Review Green was added to RAC2. Added phenotypes Reticular dysgenesis; poststreptococcal glomerulonephritis; Congenital defects of phagocyte number or function; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Recurrent sinopulmonary infections, selective IgA defiency; urticaria; T-B- SCID; Poor wound healing, leukocytosis for gene: RAC2 Rating Changed from Amber List (moderate evidence) to Green List (high evidence) |
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| COVID-19 research v0.36 | RAC2 |
Ellen McDonagh gene: RAC2 was added gene: RAC2 was added to Viral susceptibility. Sources: Combined B and T cell defect v1.12,ESID Registry 20171117,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,SCID v1.6,IUIS Classification February 2018,Expert Review Amber Mode of inheritance for gene: RAC2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: RAC2 were set to 21167572; 30654050; 30723080; 31071452; 25512081; 10758162; 31382036; 10961859 Phenotypes for gene: RAC2 were set to Reticular dysgenesis; poststreptococcal glomerulonephritis; Congenital defects of phagocyte number or function; Neutrophil immunodeficiency syndrome; RAS-related C3 Bolutinum toxin substrate 2 deficiency (RAC2); T-B+ SCID; Neutrophil immunodeficiency syndrome 608203; Recurrent sinopulmonary infections, selective IgA defiency; urticaria; T-B- SCID; Poor wound healing, leukocytosis |
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| COVID-19 research v0.36 | SLC39A7 |
Ellen McDonagh gene: SLC39A7 was added gene: SLC39A7 was added to Viral susceptibility. Sources: Expert Review Red,Literature,IUIS Classification December 2019 Mode of inheritance for gene: SLC39A7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC39A7 were set to 32086639; 32048120; 30718914 Phenotypes for gene: SLC39A7 were set to Agammaglobulinemia; B cell deficiency; Early onset infections, blistering dermatosis, failure to thrive, thrombocytopenia; Predominantly Antibody Deficiencies |
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| COVID-19 research v0.36 | RC3H1 |
Ellen McDonagh gene: RC3H1 was added gene: RC3H1 was added to Viral susceptibility. Sources: Expert Review Red,Literature Mode of inheritance for gene: RC3H1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: RC3H1 were set to PMID: 31636267 Phenotypes for gene: RC3H1 were set to Hemophagocytic lymphohistiocytosis |
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| COVID-19 research v0.36 | ERCC3 |
Ellen McDonagh gene: ERCC3 was added gene: ERCC3 was added to Viral susceptibility. Sources: Victorian Clinical Genetics Services,North West GLH,NHS GMS,London North GLH,Expert Review Red Mode of inheritance for gene: ERCC3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ERCC3 were set to none Phenotypes for gene: ERCC3 were set to none |
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| COVID-19 research v0.36 | TTC37 |
Ellen McDonagh gene: TTC37 was added gene: TTC37 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,A- or hypo-gammaglobulinaemia v1.25,IUIS Classification February 2018 Mode of inheritance for gene: TTC37 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TTC37 were set to 29383842; 25688341; 28292286; 21120949; 28944135; 20176027 Phenotypes for gene: TTC37 were set to Recurrent bacterial and viral infections, Abnormal hair findings: trichorrhexis nodosa; Trichohepatoenteric syndrome 1, 222470; Intrauterine growth retardation, woolly hair; intractable diarrhoea in infancy requiring total parenteral nutrition; Hypogammaglobulinaemia; Predominantly Antibody Deficiencies; facial dysmorphism; immune dysfunction; Trichohepatoenteric syndrome |
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| COVID-19 research v0.36 | SLC37A4 |
Ellen McDonagh gene: SLC37A4 was added gene: SLC37A4 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: SLC37A4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC37A4 were set to 9428641; 10482962; 12576310 Phenotypes for gene: SLC37A4 were set to Glycogen storage disease Ib; Congenital defects of phagocyte number or function; Glycogen storage disease Ib, 232220; Glycogen storage disease type 1b (GS1b); Glycogen storage disease with or without neutropenia; Glycogen storage disease Ic; Fasting hypoglycemia, lactic acidosis, hyperlipidemia, hepatomegaly |
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| COVID-19 research v0.36 | SLC35C1 |
Ellen McDonagh gene: SLC35C1 was added gene: SLC35C1 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: SLC35C1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC35C1 were set to 11326279; 24403049; 11213799; 12116250; 11326280; 1279426 Phenotypes for gene: SLC35C1 were set to Mild LAD type 1 features with hh-blood group, growth retardation, developmental delay; Congenital defects of phagocyte number or function; Leukocyte adhesion deficiency (LAD); Congenital disorder of glycosylation, type IIc 266265 |
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| COVID-19 research v0.36 | G6PC3 |
Ellen McDonagh gene: G6PC3 was added gene: G6PC3 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,Congenital neutropaenia v1.22,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: G6PC3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: G6PC3 were set to 19118303; 20616219 Phenotypes for gene: G6PC3 were set to Structural heart defects, urogenital abnormalities, inner ear deafness, and venous angiectasias of trunks and limbs; Congenital neutropenia; Dursun syndrome, 612541; Severe Congenital Neutropenia; Neutropenia, severe congenital 4, autosomal recessive, 612541; Congenital defects of phagocyte number or function; Neutropenia, severe congenital 4 |
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| COVID-19 research v0.36 | CFI |
Ellen McDonagh gene: CFI was added gene: CFI was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,Inherited complement deficiency v0.11,NHS GMS,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: CFI was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CFI were set to 18374984; 24142231; 22710145; 19065647; 8613545; 12562389; 27091480; 3897024; 21316765; 25988862 Phenotypes for gene: CFI were set to {Macular degeneration, age-related, 13, susceptibility to}, 615439; Complement factor I deficiency; Factor I deficiency; {Hemolytic uremic syndrome, atypical, susceptibility to, 3}, 612923; Infections, disseminated neisserial infections, atypical Hemolytic-uremic syndrome, preeclampsia; Complement Deficiencies; Immunodeficiency with factor I anomaly; C3b inactivator deficiency; Complement factor I deficiency, 610984 |
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| COVID-19 research v0.36 | C3 |
Ellen McDonagh gene: C3 was added gene: C3 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: C3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: C3 were set to 1350678; 1976733; 15781264; 4117597 Phenotypes for gene: C3 were set to Complement Deficiencies; Complement component 3 deficiency; Atypical hemolytic-uremic syndrome, dense deposit disease; Infections, glomerulonephritis, atypical hemolytic-uremic syndrome with GOF mutations; C3 deficiency, 613779 |
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