Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: RFXAPComment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.Created: 14 Oct 2020, 4:22 p.m. | Last Modified: 14 Oct 2020, 4:22 p.m.
Panel Version: 2.307
The following PubMed IDs were added to gene RFXAP (OMIM gene MIM#601861): 20197681;9287230;9806639;18336911;12498778;22390233;9118943. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
Publications
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
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): RFXAP .PanelApp HGNC gene symbol check: RFXAP . IUIS Disease: MHC class II deficiency group D . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Respiratory and gastrointestinal infections, liver/biliary tract disease. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: Combined Immunodeficiencies Generally Less Profound than Severe Combined ImmunodeficiencyCreated: 2 Jul 2018, 10:35 a.m.
Ellen McDonagh (Genomics England Curator), 6 Jun 2016. PMID: 9118943 - isolation of the gene as a component of the RFX complex. Showed that the gene was mutated in a cell line and an MHC-II deficiency patient PMID: 9287230 - Two homozygous variants in the RFXAP gene were identified in 3 cell lines from 3 unrelated patients with primary MHC class II deficiency (Turkish, Moroccan, Algerian). Transfection of RFXAP restored expression of MHC class II molecules in the patients' cells PMID: 22390233 - a homozygous variant casusing a premature stop codon in the RFXAP gene was found in the RFXAP gene in a 6 month old girl with Type III Bare lymphocyte syndrome PMID: 20197681 - RFXAP deficiency in a patient reported to be due to a homozygous p.Ser123ThrfsX15 variant in RFXAP PMID: 18336911 - patient with MHC-II deficiency, lacked RFXAP mRNA expression. Homozygous 75bp insertion in the 5'UTR was identified, impairing transcription. PMID:12498778 - a homozygous premature stop codon variant was identified in the RFXAP gene in a patient from whom primary cell MHCII molecule cell surface expression was corrected using a RFXAP vector PMID: 9806639 - functional evidence for the importance of the RFX protein complex.Created: 18 Apr 2018, 3:49 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: RFXAP, PanelApp HGNC gene symbol check: RFXAP, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / HLA class II deficiency / HLA class II deficiencyCreated: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: RFXAP, GRID_Gene_Symbol: RFXAP, GRID_Transcript_ENS_Community submitted: ENST00000255476, GRID_Transcript_RefSeq: NM_000538.3, GRID_Transcript_ENS_used_on_Production: ENST00000255476Created: 17 Apr 2018, 12:12 p.m.
Comment on list classification: The gene was added by expert review, and rated green. Multiple cases, with different variants, reported with functional importance of a role in the RFX protein complex.Created: 6 Jun 2016, 1:47 p.m.
Gene: rfxap has been classified as Green List (High Evidence).
Source Other was added to RFXAP. Publications for gene RFXAP were updated from 9118943; 9287230; 22390233; 20197681; 18336911; 12498778; 9806639 to 22390233; 9118943; 9806639; 9806639; 9287230; 18336911; 20197681; 12498778 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to RFXAP.
Source North West GLH was added to RFXAP.
Source London North GLH was added to RFXAP.
2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.
Phenotypes for gene RFXAP were set to Bare lymphocyte syndrome, type II, complementation group D, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome), HLA class II deficiency, Respiratory and gastrointestinal infections, liver/biliary tract disease, Immunodeficiencies affecting cellular and humoral immunity
IUIS Classification February 2018 was added to RFXAP. Panel: Primary immunodeficiency disorders
Victorian Clinical Genetics Services was added to RFXAP. Panel: Primary immunodeficiency disorders
Gene: rfxap has been classified as Green List (High Evidence).
ESID Registry 20171117 was added to RFXAP. Panel: Primary immunodeficiency disorders Phenotypes for gene RFXAP were set to Bare lymphocyte syndrome, type II, complementation group D, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome), HLA class II deficiency
Phenotypes for gene RFXAP were set to Bare lymphocyte syndrome, type II, complementation group D, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome)
GRID V2.0 was added to RFXAP. Panel: Primary immunodeficiency disorders Phenotypes for gene RFXAP were set to Bare lymphocyte syndrome, type II, complementation group D, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome)
RFXAP Source: GOSH PID 20171189 was removed from gene: RFXAP
GOSH PID v.8.0 was added to RFXAP. Panel: Primary immunodeficiency disorders
GOSH PID 20171189 was added to RFXAP. Panel: Primary immunodeficiency disorders
RFXAP was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12
RFXAP was created by Louise Daugherty