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Primary immunodeficiency

Gene: RFXANK

Green List (high evidence)

RFXANK (regulatory factor X associated ankyrin containing protein)
EnsemblGeneIds (GRCh38): ENSG00000064490
EnsemblGeneIds (GRCh37): ENSG00000064490
OMIM: 603200, Gene2Phenotype
RFXANK is in 4 panels

6 reviews

Eleanor Williams (Genomics England Curator)

Comment 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: 2.306
The following PubMed IDs were added to gene RFXANK (OMIM gene MIM#603200): 11313409;12618906;9806546;20414676;22863278. 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

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): RFXANK .PanelApp HGNC gene symbol check: RFXANK . IUIS Disease: MHC class II deficiency group B . IUIS Inheritance: AR .T cells: Normal or Increased activated T cells, .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.
Review made by Ellen McDonagh (Genomics England Curator) 6 Jun 2016, 11:51 a.m. PMID: 11313409 - case study of a North African patient with MHC class II deficiency homozygous 1-bp transversion (G to C) that abolished the splice site downstream of exon 4 of the RFXANK gene PMID:12618906 - two novel missense variants PMID: 22863278 - 9 out of 11 unrelated Algerian patients with histocompatibility complex class II expression deficiency had a 26 bp deletion (named I5E6-25_I5E6+1, also known as 752delG26). PMID: 20414676 - ten unrelated Moroccan patients with MHC class II deficiency all had the same homozygous 752delG26 mutation. PMID: 9806546 - functional evidence
Created: 18 Apr 2018, 3:48 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: RFXANK, PanelApp HGNC gene symbol check: RFXANK, 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: RFXANK, GRID_Gene_Symbol: RFXANK, GRID_Transcript_ENS_Community submitted: ENST00000303088, GRID_Transcript_RefSeq: NM_003721.3, GRID_Transcript_ENS_used_on_Production: ENST00000303088
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: Gene added by a reviewer and rated green. Large deletions in this gene have been reported in patients of North African origin, however missense and splice variants have also been reported.

Created: 6 Jun 2016, 10:51 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • GOSH PID v.8.0
  • Combined B and T cell defect v1.12
Phenotypes
  • MHC class II deficiency, complementation group B
  • 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
OMIM
603200
Clinvar variants
Variants in RFXANK
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: rfxank has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to RFXANK. Publications for gene RFXANK were updated from 11313409; 12618906; 22863278; 20414676; 9806546 to 20414676; 9806546; 12618906; 22863278; 11313409 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to RFXANK.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to RFXANK.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to RFXANK.

12 Jul 2018, Gel status: 4

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

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.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene RFXANK were set to MHC class II deficiency, complementation group B, 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

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to RFXANK. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to RFXANK. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: rfxank has been classified as Green List (High Evidence).

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to RFXANK. Panel: Primary immunodeficiency disorders Phenotypes for gene RFXANK were set to MHC class II deficiency, complementation group B, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome), HLA class II deficiency

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene RFXANK were set to MHC class II deficiency, complementation group B, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome)

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to RFXANK. Panel: Primary immunodeficiency disorders Phenotypes for gene RFXANK were set to MHC class II deficiency, complementation group B, Combined immunodeficiency (MHC class II deficiency, bare lymphocyte syndrome)

6 Apr 2018, Gel status: 4

Clear Sources

Louise Daugherty (Genomics England Curator)

RFXANK Source: GOSH PID 20171188 was removed from gene: RFXANK

6 Apr 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to RFXANK. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID 20171188 was added to RFXANK. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

RFXANK was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

RFXANK was created by Louise Daugherty