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Primary immunodeficiency

Gene: CD79B

Green List (high evidence)

CD79B (CD79b molecule)
EnsemblGeneIds (GRCh38): ENSG00000007312
EnsemblGeneIds (GRCh37): ENSG00000007312
OMIM: 147245, Gene2Phenotype
CD79B is in 3 panels

6 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

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): CD79B .PanelApp HGNC gene symbol check: CD79B . IUIS Disease: Igb deficiency . IUIS Inheritance: AR .T cells: Low CD4 cells Absent MHC II expression on lymphocytes, B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Severe bacterial infections, normal numbers of pro-B cells. IUIS Major category: Predominantly Antibody Deficiencies. IUIS Subcategory: Severe Reduction in All Serum Immunoglobulin Isotypes with Profoundly Decreased or Absent B Cells, Agammaglobulinemia.
Created: 2 Jul 2018, 11:03 a.m.
Comment on list classification: Changed from Amber to Green - three unrelated cases with PID phenotype described in the literature. PMID:17675462 (2007), PMID:17709424 (2007), PMID:24722855 (2014)
Created: 4 May 2018, 5:10 p.m.
The first female case with Igbeta deficiency carried a homozygous Q80X nonsense mutation., of Austrian descent, described (PMID:17675462) carried a homozygous G137S missense mutation
The second case, of Italian origin, affected with Igbeta deficiency (PMID: 17709424) carried a homozygous Q80X nonsense mutation.
The third case (PMID: 24722855) describes the third case worldwide of autosomal recessive agammaglobulinemia due to a novel non-sense mutation in Ig beta presenting with neutropenia, ecthyma and mild respiratory infections. The patient was born to consanguineous parents of Tunisian ethnicity.
Created: 4 May 2018, 5:03 p.m.
Comment on publications: Added publications to support the PID phenotype
Created: 4 May 2018, 4:58 p.m.
Comment on phenotypes: added phenotypes from publications
Created: 4 May 2018, 4:52 p.m.
The largest group of patients has X-linked agammaglobulinemia (XLA), which is a caused by a defect in the BTK gene encoding Bruton Tyrosine Kinsase (Btk), which accounts for 85% of agammaglobulinemia patients. A smaller group has defects in for instance IGLL1, CD79A, CD79B, or BLNK, which have clinical findings that are similar from those seen in patients with mutations in Btk but tend to have a more severe onset of disease. These were forms of agammaglobulinemia with autosomal recessive inheritance (ARA). All of these genes code for proteins that work with BTK to support the maturation of pro-B-cells into pre-B-cells. Patients with mutations in any of these genes have clinical and laboratory findings that are very similar to those seen in patients with mutations in BTK.
Created: 4 May 2018, 4:49 p.m.
This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Red. The gene is present in the 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: CD79B, PanelApp HGNC gene symbol check: CD79B, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Predominantly antibody disorders / Agammaglobulinemias / Agammaglobulinemia
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: CD79B, GRID_Gene_Symbol: CD79B, GRID_Transcript_ENS_Community submitted: ENST00000392795, GRID_Transcript_RefSeq: NM_001039933.1, GRID_Transcript_ENS_used_on_Production: ENST00000392795
Created: 17 Apr 2018, 12:12 p.m.

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

Peter Arkwright (Royal Manchester Foundation Trust)

Green List (high evidence)

Sophie Hambleton (Newcastle University)

Red List (low evidence)

only 2 cases described so caution required
Created: 6 Jan 2017, 3:16 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Two positive expert reviews and one negative. No association with disease on Gen2Phen. Two homozygous LOF variants reported in the literature
Created: 11 May 2016, 9:34 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • ESID Registry 20171117
  • GRID V2.0
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • Agammaglobulinemia 6, 612692
  • Agammaglobulinemia 6
  • Agammaglobulinemia
  • CD79B deficiency, Agammaglobulinemia with autosomal recessive inheritance (ARA)
  • Severe bacterial infections, normal numbers of pro-B cells
  • Predominantly Antibody Deficiencies
OMIM
147245
Clinvar variants
Variants in CD79B
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to CD79B.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to CD79B.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to CD79B.

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 CD79B were set to Agammaglobulinemia 6, 612692, Agammaglobulinemia 6, Agammaglobulinemia, CD79B deficiency, Agammaglobulinemia with autosomal recessive inheritance (ARA), Severe bacterial infections, normal numbers of pro-B cells, Predominantly Antibody Deficiencies

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to CD79B. 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 CD79B. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: cd79b has been classified as Green List (High Evidence).

4 May 2018, Gel status: 3

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

4 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CD79B were set to 17675462; 17709424; 24722855

4 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CD79B were set to Agammaglobulinemia 6, 612692; Agammaglobulinemia 6; Agammaglobulinemia; CD79B deficiency, Agammaglobulinemia with autosomal recessive inheritance (ARA)

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to CD79B. 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 CD79B. Panel: Primary immunodeficiency disorders Phenotypes for gene CD79B were set to Agammaglobulinemia 6, 612692, Agammaglobulinemia 6, Agammaglobulinemia

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CD79B were set to Agammaglobulinemia 6, 612692, Agammaglobulinemia 6

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to CD79B. Panel: Primary immunodeficiency disorders Phenotypes for gene CD79B were set to Agammaglobulinemia 6, 612692, Agammaglobulinemia 6

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

CD79B was added to Primary immunodeficiency disorders panel. Sources: Expert Review Red, A- or hypo-gammaglobulinaemia v1.25

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

CD79B was created by Louise Daugherty