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Primary immunodeficiency

Gene: B2M

Green List (high evidence)

B2M (beta-2-microglobulin)
EnsemblGeneIds (GRCh38): ENSG00000166710
EnsemblGeneIds (GRCh37): ENSG00000166710
OMIM: 109700, Gene2Phenotype
B2M is in 5 panels

5 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, 12:25 p.m. | Last Modified: 14 Oct 2020, 12:25 p.m.
Panel Version: 2.223
The following PubMed IDs were added to gene B2M (OMIM gene MIM#109700): 4186801;25702838. 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)

Single kindred (2 patients) so far described but high confidence in pathomechanism
Created: 19 Jun 2018, 5:25 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

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): B2M .PanelApp HGNC gene symbol check: B2M . IUIS Disease: MHC class I deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Sinopulmonary infections, cutaneous granulomas. Absent _2m associated proteins MHC-I, CD1a, CD1b, CD1c . 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.
Comment on list classification: Changed Amber to Green from external review comment
Created: 20 Jun 2018, 2:52 p.m.
Reviewed and decided to keep amber until more info on gene and disease association. Currently only 2 sibs reported in the literature last report in 2015 PMID:25702838
Created: 11 May 2018, 2:04 p.m.
Comment on phenotypes: added phenotype from OMIM MIMd and Orphanet : Immunodeficiency by defective expression of HLA class 1 is a very rare, primary, genetic, immunodeficiency disorder characterized by partial or complete absence of human leukocyte antigen class I expression resulting in a non-specific clinical picture of impaired immune response and susceptibility to infections.
Created: 11 May 2018, 1:46 p.m.
Comment on publications: Added publications to support the PID phenotype, PMID: 4186801 (2 sibs affected) and another but unrelated family PMID:25702838 (2 sibs affected)
Created: 11 May 2018, 1:45 p.m.
Comment on mode of inheritance: changed MOI to Biallelic as it it the Immunodeficiency 43 phenotype and not Amyloidosis, familial visceral phenotype (AD) that is repreented on this panel
Created: 11 May 2018, 1:40 p.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 supplied by GRID. GRID Gene Symbol HGNC PanelApp check: B2M, GRID_Gene_Symbol: B2M, GRID_Transcript_ENS_Community submitted: ENST00000558401, GRID_Transcript_RefSeq: NM_004048.2, GRID_Transcript_ENS_used_on_Production: ENST00000558401
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
  • GRID V2.0
Phenotypes
  • Immunodeficiency 43,241600
  • Immunodeficiency by defective expression of HLA class 1
  • Sinopulmonary infections, cutaneous granulomas. Absent _2m associated proteins MHC-I, CD1a, CD1b, CD1c
  • Immunodeficiencies affecting cellular and humoral immunity
OMIM
109700
Clinvar variants
Variants in B2M
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: b2m 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 B2M. Publications for gene B2M were updated from 4186801; 25702838 to 25702838; 4186801 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 B2M.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to B2M.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to B2M.

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 B2M were set to Immunodeficiency 43,241600, Immunodeficiency by defective expression of HLA class 1, Sinopulmonary infections, cutaneous granulomas. Absent _2m associated proteins MHC-I, CD1a, CD1b, CD1c, 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 B2M. 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 B2M. Panel: Primary immunodeficiency disorders

20 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: b2m has been classified as Green List (High Evidence).

20 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: b2m has been classified as Green List (High Evidence).

11 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for B2M were set to Immunodeficiency 43,241600; Immunodeficiency by defective expression of HLA class 1

11 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for B2M were set to 4186801; 25702838

11 May 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for B2M was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to B2M. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene B2M were set to Immunodeficiency 43

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

B2M was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

B2M was created by Louise Daugherty