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COVID-19 research

Gene: RFXAP

Green List (high evidence)

RFXAP (regulatory factor X associated protein)
EnsemblGeneIds (GRCh38): ENSG00000133111
EnsemblGeneIds (GRCh37): ENSG00000133111
OMIM: 601861, Gene2Phenotype
RFXAP is in 3 panels

5 reviews

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

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
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 Immunodeficiency
Created: 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 deficiency
Created: 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: ENST00000255476
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Ellen McDonagh (Genomics England Curator)

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.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • HLA class II deficiency
  • Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome)
  • Bare lymphocyte syndrome, type II, complementation group D
  • Immunodeficiencies affecting cellular and humoral immunity
  • Respiratory and gastrointestinal infections, liver/biliary tract disease
OMIM
601861
Clinvar variants
Variants in RFXAP
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Apr 2020, Gel status: 3

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

Ellen McDonagh (Genomics England Curator)

gene: RFXAP was added gene: RFXAP was added to Viral susceptibility. Sources: Expert Review Green,Combined B and T cell defect v1.12,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: RFXAP was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: RFXAP were set to 12498778; 9287230; 18336911; 22390233; 20197681; 9118943; 9806639 Phenotypes for gene: RFXAP were set to HLA class II deficiency; Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome); Bare lymphocyte syndrome, type II, complementation group D; Immunodeficiencies affecting cellular and humoral immunity; Respiratory and gastrointestinal infections, liver/biliary tract disease