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Primary immunodeficiency

Gene: CR2

Amber List (moderate evidence)

CR2 (complement C3d receptor 2)
EnsemblGeneIds (GRCh38): ENSG00000117322
EnsemblGeneIds (GRCh37): ENSG00000117322
OMIM: 120650, Gene2Phenotype
CR2 is in 3 panels

4 reviews

Louise Daugherty (Genomics England Curator)

I don't know

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): CR2 .PanelApp HGNC gene symbol check: CR2 . IUIS Disease: CD21 deficiency . IUIS Inheritance: AR .T cells: Low, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Recurrent infections. IUIS Major category: Predominantly Antibody Deficiencies. IUIS Subcategory: Severe Reduction in at Least 2 Serum Immunoglobulin Isotypes with Normal or Low Number of B Cells, CVID Phenotype
Created: 2 Jul 2018, 10:35 a.m.
Reviewed again and decided to keep as Amber, there are some conflict regarding the pertinence, still only two cases reported in the literature, and in addition to this, in Clinvar (July 2017) there are conflicting interpretations of pathogenicity reported in some clinical labs worldwide: Likely benign (Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine and ARUP Laboratories, Molecular Genetics and Genomics);Uncertain significance (Invitae), the gene-disease is not that strong.
Created: 9 May 2018, 12:36 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: CD21, PanelApp HGNC gene symbol check: CR2, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Predominantly antibody disorders / Hypogammaglobulinemias / Common variable immunodeficiency disorders (CVID); Predominantly antibody disorders / Hypogammaglobulinemias / Isolated IgG subclass deficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: CR2, GRID_Gene_Symbol: CR2, GRID_Transcript_ENS_Community submitted: ENST00000367057, GRID_Transcript_RefSeq: NM_001006658.2, GRID_Transcript_ENS_used_on_Production: ENST00000367057
Created: 17 Apr 2018, 12:12 p.m.

Peter Arkwright (Royal Manchester Foundation Trust)

Green List (high evidence)

Sophie Hambleton (Newcastle University)

Red List (low evidence)

2 patients described only so caution required
Created: 6 Jan 2017, 3:18 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
hypogammaglobulinaemia

Publications

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: One positive and one negative expert review. No disease associated on Gen2Phen. Two LOF variant identified in two compound heterozygotes.
Created: 11 May 2016, 9:39 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • A- or hypo-gammaglobulinaemia v1.25
Phenotypes
  • Immunodeficiency, common variable, 7, 614699
  • Lupus
  • Immunodeficiency, common variable, 7
  • Common variable immunodeficiency disorders (CVID)
  • Isolated IgG subclass deficiency
  • hypogammaglobulinaemia
  • Recurrent infections
  • Predominantly Antibody Deficiencies
OMIM
120650
Clinvar variants
Variants in CR2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

12 Jul 2018, Gel status: 2

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.

6 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: cr2 has been classified as Amber List (Moderate Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CR2 were set to Immunodeficiency, common variable, 7, 614699, Lupus, Immunodeficiency, common variable, 7, Common variable immunodeficiency disorders (CVID), Isolated IgG subclass deficiency, hypogammaglobulinaemia, Recurrent infections, Predominantly Antibody Deficiencies

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to CR2. 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 CR2. Panel: Primary immunodeficiency disorders

9 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CR2 were set to 22035880; 26325596

20 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CR2 were set to Immunodeficiency, common variable, 7, 614699; Lupus; Immunodeficiency, common variable, 7; Common variable immunodeficiency disorders (CVID); Isolated IgG subclass deficiency; hypogammaglobulinaemia

20 Apr 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CR2 were set to Immunodeficiency, common variable, 7, 614699; Lupus; Immunodeficiency, common variable, 7; Immunodeficiency, common variable, 7; Common variable immunodeficiency disorders (CVID); Isolated IgG subclass deficiency; hypogammaglobulinaemia

20 Apr 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CR2 were set to 16672701; 22035880; 26325596

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to CR2. 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 CR2. Panel: Primary immunodeficiency disorders Phenotypes for gene CR2 were set to Immunodeficiency, common variable, 7, 614699, Lupus, Immunodeficiency, common variable, 7, Immunodeficiency, common variable, 7, Common variable immunodeficiency disorders (CVID), Isolated IgG subclass deficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CR2 were set to Immunodeficiency, common variable, 7, 614699, Lupus, Immunodeficiency, common variable, 7, Immunodeficiency, common variable, 7

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to CR2. Panel: Primary immunodeficiency disorders Phenotypes for gene CR2 were set to Immunodeficiency, common variable, 7, 614699, Lupus, Immunodeficiency, common variable, 7

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

CR2 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)

CR2 was created by Louise Daugherty