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Primary immunodeficiency

Gene: RBCK1

Green List (high evidence)

RBCK1 (RANBP2-type and C3HC4-type zinc finger containing 1)
EnsemblGeneIds (GRCh38): ENSG00000125826
EnsemblGeneIds (GRCh37): ENSG00000125826
OMIM: 610924, Gene2Phenotype
RBCK1 is in 11 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, 4:20 p.m. | Last Modified: 14 Oct 2020, 4:20 p.m.
Panel Version: 2.304
The following PubMed IDs were added to gene RBCK1 (OMIM gene MIM#610924): 23798481;610924. 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

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
bacterial infections, autoinflammation, amylopectinosis

Publications

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 8 variants identified in unrelated cases, however, only 2 cases had Polyglucosan body myopathy 1 with immunodeficiency.
Created: 9 May 2018, 2:55 p.m.

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
Comment on list classification: Changed Amber to Green from external expert review and further publications to support gene-disease association (more than three cases with immunodeficiency
Created: 5 Jul 2018, 10:54 a.m.
Krenn M et al (2018) PMID: 29260357 describe two new patients with pathogenic mutations in the RBCK1 gene expanding the total number of known families with this condition in the literature from 12 to 14. They confirmed the few previous reports insofar as both a myopathy and an immunological phenotype are part of the clinical spectrum of RBCK1-associated disease. It was suggested that the exact localization of the mutation within the gene might be responsible for the specific phenotype, with N-terminal mutations causing severe immunological dysfunction and mutations in the middle or C-terminal part leading to a myopathy phenotype. They reported the clinical, immunological and genetic findings of two unrelated individuals suffering from a childhood-onset RBCK1-asscociated disease caused by the same homozygous truncating mutation (NM_031229.2:c.896_899del, p.Glu299Valfs*46) in the middle part of the RBCK1 gene. The patients suffered from a myopathy with cardiac involvement, but in contrast to previous reports on mutations in this part of the gene, also displayed signs of autoinflammation and immunodeficiency. The report suggests that RBCK1 mutations at locations that were previously thought to lack immunological features may also present with immunological dysfunction later in the disease course.
Created: 5 Jul 2018, 10:52 a.m.
Comment on publications: Added publications to support gene-disease association, and upgrading of the gene to Green.
Created: 5 Jul 2018, 10:52 a.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): HOIL1 (RBCK1) .PanelApp HGNC gene symbol check: RBCK1 . IUIS Disease: HOIL1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, decreased memory B cells, .IUIS Other affected cells: N/A. IUIS Associated features: Bacterial infections, autoinflammation, amylopectinosis . IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Other Combined immunodeficiencies with associated or syndromic features
Created: 2 Jul 2018, 10:35 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: HOIL1, PanelApp HGNC gene symbol check: RBCK1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Autoinflammatory disorders / Other autoinflammatory diseases with known genetic defect / Other autoinflammatory diseases with known genetic defect; Defects in innate immunity / HOIL1 deficiency / HOIL1 deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: RBCK1, GRID_Gene_Symbol: RBCK1, GRID_Transcript_ENS_Community submitted: ENST00000356286, GRID_Transcript_RefSeq: NM_031229.2, GRID_Transcript_ENS_used_on_Production: ENST00000356286
Created: 17 Apr 2018, 12:12 p.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
Phenotypes
  • Polyglucosan body myopathy, early-onset, with or without immunodeficiency 615895
  • Other autoinflammatory diseases with known genetic defect
  • HOIL1 deficiency
  • Bacterial infections, autoinflammation, amylopectinosis
  • Combined immunodeficiencies with associated or syndromic features
OMIM
610924
Clinvar variants
Variants in RBCK1
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: rbck1 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 RBCK1. Publications for gene RBCK1 were updated from 23104095; 29260357 to 23798481; 610924; 29260357; 23104095 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 RBCK1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to RBCK1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to RBCK1.

12 Jul 2018, Gel status: 3

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.

5 Jul 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: rbck1 has been classified as Green List (High Evidence).

5 Jul 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: rbck1 has been classified as Green List (High Evidence).

5 Jul 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: RBCK1 were set to 23104095; 29260357

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene RBCK1 were set to Polyglucosan body myopathy, early-onset, with or without immunodeficiency 615895, Other autoinflammatory diseases with known genetic defect, HOIL1 deficiency, Bacterial infections, autoinflammation, amylopectinosis, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to RBCK1. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to RBCK1. Panel: Primary immunodeficiency disorders

9 May 2018, Gel status: 2

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

9 May 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for RBCK1 were set to 23104095

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for RBCK1 were set to Polyglucosan body myopathy, early-onset, with or without immunodeficiency 615895; Other autoinflammatory diseases with known genetic defect; HOIL1 deficiency

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to RBCK1. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to RBCK1. Panel: Primary immunodeficiency disorders Phenotypes for gene RBCK1 were set to Polyglucosan body myopathy, early-onset, with or without immunodeficiency, Other autoinflammatory diseases with known genetic defect, HOIL1 deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene RBCK1 were set to Polyglucosan body myopathy, early-onset, with or without immunodeficiency

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

RBCK1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

RBCK1 was created by Louise Daugherty