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Primary immunodeficiency

Gene: CSF3R

Green List (high evidence)

CSF3R (colony stimulating factor 3 receptor)
EnsemblGeneIds (GRCh38): ENSG00000119535
EnsemblGeneIds (GRCh37): ENSG00000119535
OMIM: 138971, Gene2Phenotype
CSF3R is in 6 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

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

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): CSF3R .PanelApp HGNC gene symbol check: CSF3R . IUIS Disease: G-CSF receptor deficiency . IUIS Inheritance: AR .T cells: Profound depletion of CD4+ cells, .B cells: N/A, .IUIS Other affected cells: N. IUIS Associated features: N/A. IUIS Major category: Congenital defects of phagocyte number or function. IUIS Subcategory: Congenital Neutropenias
Created: 2 Jul 2018, 10:35 a.m.
Comment on list classification: changed from Amber to Green after internal clinical review. The monoallelic form associated with neutrophilia is not relevant to this panel. However, there is a reference to three unrelated families with severe congenital neutropaenia and biallelic variants in OMIM, so rate Green
Created: 11 May 2018, 3:51 p.m.
Comment on publications: Three unrelated affecteds have been reported with Severe congenital neutropenia-7 caused by variants in CSF3R (PMID:24753537 (2104) , PMID:26324699 (2015). However, the main therapy of Severe congenital neutropenia (SCN) is the application of granulocyte colony stimulating factor (G-CSF). CSF3R gene mutation often occurs in the treatment process, and can lead to acute myeloid leukemia. (PMID: 29070147)
Created: 9 May 2018, 1:52 p.m.
Comment on mode of inheritance: Changed from monoallelic to biallelic inheritance as this instance represents Neutropenia, severe congenital, 7, autosomal recessive, 617014, which is relevant to this panel and not Hereditary neutrophilia, 617014 which was noted as being Autosomal dominant, the phenotype of which is not relevant to this panel
Created: 9 May 2018, 1:29 p.m.
Comment on phenotypes: Also reported gene-phenotype Neutrophilia, hereditary,162830 from OMIM PMID:19620628 Plo et al. (2009) who found a 3-generation family segregating autosomal dominant neutrophilia, sequenced the CSF3R gene and identified a heterozygous activating mutation.This phenotype is not relevant to the PID panel.
Created: 9 May 2018, 1:20 p.m.
Comment on phenotypes: From expert review it was noted that somatic mutations of this gene often occur following GCSF therapy for severe congenital neutropenia of alternative aetiology, but germline mutations of CSF3R are associated with neutrophilia rather than neutropenia. The germline mutations result in a phenotype that is not PID panel relevant.
Created: 9 May 2018, 12:55 p.m.
Associated in the ESID Registry to a PID Diagnosis of Phagocytic disorders Congenital neutropenia, but from the literature and expert reviews CSF3R germline mutations are associated to neutrophilia rather than neutropenia.
Created: 9 May 2018, 12:50 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: CSF3R, PanelApp HGNC gene symbol check: CSF3R, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Phagocytic disorders / Congenital neutropenia / Congenital neutropenia
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: CSF3R, GRID_Gene_Symbol: CSF3R, GRID_Transcript_ENS_Community submitted: ENST00000373103, GRID_Transcript_RefSeq: NM_156039.3, GRID_Transcript_ENS_used_on_Production: ENST00000373103
Created: 17 Apr 2018, 12:12 p.m.

Publications

Peter Arkwright (Royal Manchester Foundation Trust)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: One expert reviewer suggested green and one red because germline variants in this gene associated with neurtophilia and not neutropenia. Associated with neurtophilia in OMIM. No disease association in G2P, and only found in 1/4 sources
Created: 24 May 2016, 8:03 p.m.

Sophie Hambleton (Newcastle University)

Red List (low evidence)

Agree there is good evidence that biallelic variation in this gene causes SCN
Created: 23 Oct 2019, 6:31 a.m. | Last Modified: 23 Oct 2019, 6:31 a.m.
Panel Version: 1.132
Somatic mutations of this gene often occur following GCSF therapy for severe congenital neutropenia of alternative aetiology, but germline mutations of CSF3R are associated with neutrophilia rather than neutropenia
Created: 19 Oct 2015, 10:35 p.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
  • Congenital neutropaenia v1.22
Phenotypes
  • Neutropenia, severe congenital, 7, autosomal recessive, 617014
  • Neutropenia, severe congenital 7
  • Congenital neutropenia
  • N/A
  • Congenital defects of phagocyte number or function
OMIM
138971
Clinvar variants
Variants in CSF3R
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 CSF3R.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to CSF3R.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to CSF3R.

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 CSF3R were set to Neutropenia, severe congenital, 7, autosomal recessive, 617014, Neutropenia, severe congenital 7, Congenital neutropenia, N/A, Congenital defects of phagocyte number or function

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to CSF3R. 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 CSF3R. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: csf3r has been classified as Green List (High Evidence).

11 May 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CSF3R were set to 24753537; 26324699; 29070147; 19620628

11 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).

9 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CSF3R were set to 24753537; 26324699; 29070147

9 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CSF3R were set to 24753537; 26324699

9 May 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for CSF3R were set to 24753537; 26324699

9 May 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for CSF3R was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal

9 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CSF3R were set to Neutropenia, severe congenital, 7, autosomal recessive, 617014; Neutropenia, severe congenital 7; Congenital neutropenia

9 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CSF3R were set to Neutropenia, severe congenital, 7, autosomal recessive, 617014; Neutropenia, severe congenital 7; Congenital neutropenia

9 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CSF3R were set to Neutrophilia, hereditary,162830; Hereditary neutrophilia

9 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CSF3R were set to Neutrophilia, hereditary,162830

9 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for CSF3R were set to Neutrophilia, hereditary, 162830; Severe congenital neutropenia; Neutropenia, severe congenital 7; Congenital neutropenia

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to CSF3R. 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 CSF3R. Panel: Primary immunodeficiency disorders Phenotypes for gene CSF3R were set to Neutrophilia, hereditary, 162830, Severe congenital neutropenic, Neutropenia, severe congenital 7, Congenital neutropenia

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CSF3R were set to Neutrophilia, hereditary, 162830, Severe congenital neutropenic, Neutropenia, severe congenital 7

17 Apr 2018, Gel status: 1

Added New Source, Set mode of inheritance, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to CSF3R. Panel: Primary immunodeficiency disorders Model of inheritance for gene CSF3R was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene CSF3R were set to Neutrophilia, hereditary, 162830, Severe congenital neutropenic, Neutropenia, severe congenital 7

29 Mar 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

CSF3R was added to Primary immunodeficiency disorders panel. Sources: Expert Review Red, Congenital neutropaenia v1.22

29 Mar 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

CSF3R was created by Louise Daugherty