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Primary immunodeficiency

Gene: LRBA

Green List (high evidence)

LRBA (LPS responsive beige-like anchor protein)
EnsemblGeneIds (GRCh38): ENSG00000198589
EnsemblGeneIds (GRCh37): ENSG00000198589
OMIM: 606453, Gene2Phenotype
LRBA is in 13 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, 1:18 p.m. | Last Modified: 14 Oct 2020, 1:18 p.m.
Panel Version: 2.273
The following PubMed IDs were added to entity LRBA: 25931386;26707784;22608502;26768763. These publications have been associated with OMIM phenotype MIM#614700, which is listed for this entity, by the immunedysregulation 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)

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotypes in OMIM and as probable Gen2Phen gene. At least 6 biallelic variants reported in 6 unrelated families
Created: 30 Apr 2018, 1:37 p.m.
Comment on phenotypes: Combined immunodeficiency; ALPS-like disease; IBD-like; IPEX-like disease; Common variable immunodeficiency disorders (CVID); Unclassified antibody deficiency
Created: 30 Apr 2018, 1:33 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
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LRBA .PanelApp HGNC gene symbol check: LRBA . IUIS Disease: LRBA deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Low or normal numbers of B cells, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent infections, inflammatory bowel disease, autoimmunity, EBV infections. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Regulatory T Cell Defects
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: LRBA, PanelApp HGNC gene symbol check: LRBA, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency; Diseases of immune dysregulation / Autoimmune lymphoproliferative syndrome (ALPS) / ALPS-like disease; ; Diseases of immune dysregulation / IPEX / IPEX-like disease Diseases of immune dysregulation / Early-onset inflammatory bowel disease / IBD-like disease; Predominantly antibody disorders / Hypogammaglobulinemias / Common variable immunodeficiency disorders (CVID); Predominantly antibody disorders / Unclassified antibody deficiency / Unclassified antibody deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: LRBA, GRID_Gene_Symbol: LRBA, GRID_Transcript_ENS_Community submitted: ENST00000357115, GRID_Transcript_RefSeq: NM_006726.4, GRID_Transcript_ENS_used_on_Production: ENST00000357115
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
  • GOSH PID v.8.0
Phenotypes
  • Immunodeficiency, common variable, 8, with autoimmunity, 614700
  • Unclassified antibody deficiency
  • Recurrent infections, inflammatory bowel disease, autoimmunity, EBV infections
  • Diseases of Immune Dysregulation
OMIM
606453
Clinvar variants
Variants in LRBA
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: lrba 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 LRBA. Publications for gene LRBA were updated from 22608502; 25468195; 22721650 to 26768763; 25468195; 25931386; 22608502; 22721650; 26707784 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 LRBA.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to LRBA.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to LRBA.

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 LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity, 614700, Unclassified antibody deficiency, Recurrent infections, inflammatory bowel disease, autoimmunity, EBV infections, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

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

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

2 May 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity, 614700; Unclassified antibody deficiency

30 Apr 2018, Gel status: 3

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

30 Apr 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for LRBA were set to 22608502; 25468195; 22721650

30 Apr 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for LRBA were set to 22608502

30 Apr 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity 614700

30 Apr 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity 614700; Combined immunodeficiency; ALPS-like disease; IBD-like; IPEX-like disease; Common variable immunodeficiency disorders (CVID); Unclassified antibody deficiency

30 Apr 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity 614700; Combined immunodeficiency; ALPS-like disease; IBD-like; IPEX-like disease; Common variable immunodeficiency disorders (CVID); Unclassified antibody deficiency

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to LRBA. 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 LRBA. Panel: Primary immunodeficiency disorders Phenotypes for gene LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity, Combined immunodeficiency, ALPS-like disease, IBD-like, IPEX-like disease, Common variable immunodeficiency disorders (CVID), Unclassified antibody deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to LRBA. Panel: Primary immunodeficiency disorders Phenotypes for gene LRBA were set to Immunodeficiency, common variable, 8, with autoimmunity

6 Apr 2018, Gel status: 1

Clear Sources

Louise Daugherty (Genomics England Curator)

LRBA Source: GOSH PID 20171167 was removed from gene: LRBA

6 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

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

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

LRBA was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171167

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

LRBA was created by Louise Daugherty