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Primary immunodeficiency

Gene: CXCR4

Green List (high evidence)

CXCR4 (C-X-C motif chemokine receptor 4)
EnsemblGeneIds (GRCh38): ENSG00000121966
EnsemblGeneIds (GRCh37): ENSG00000121966
OMIM: 162643, Gene2Phenotype
CXCR4 is in 5 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): CXCR4 .PanelApp HGNC gene symbol check: CXCR4 . IUIS Disease: WHIM (Warts, Hypogammaglobulinemia, infections, Myelokathexis) syndrome . IUIS Inheritance: AD GOF .T cells: Increased DN T cells , .B cells: N/A, .IUIS Other affected cells: Granulocytes + Lymphocytes. IUIS Associated features: Warts (HPV) infection, neutropenia, low B cell number, hypogammaglobulinemia. IUIS Major category: Defects in Intrinsic and Innate Immunity. IUIS Subcategory: Epidermodysplasia verruciformis (HPV)
Created: 2 Jul 2018, 10:35 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: CXCR4, PanelApp HGNC gene symbol check: CXCR4, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Defects in innate immunity / Warts hypogammaglobulinemia infections and myelokathexis (WHIM) / Warts hypogammaglobulinemia infections and myelokathexis (WHIM)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: CXCR4, GRID_Gene_Symbol: CXCR4, GRID_Transcript_ENS_Community submitted: ENST00000409817, GRID_Transcript_RefSeq: NM_003467.2, GRID_Transcript_ENS_used_on_Production: ENST00000409817
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
WHIM syndrome - warts, hypogammaglobulinaemia, infections, myelokathexis

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

Peter Arkwright (Royal Manchester Foundation Trust)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Found associated with phenotype in OMIM, not in G2P. Two expert reviewers recommend Green. Four terminating variants found in unrelated families in the literature.
Created: 25 May 2016, 9:20 a.m.
Comment on publications: Four terminating variants found in unrelated families
Created: 25 May 2016, 9:11 a.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
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
  • WHIM syndrome, 193670
  • Myelokathexis, isolated
  • WHIM syndrome
  • Warts hypogammaglobulinemia infections and myelokathexis (WHIM)
  • Warts (HPV) infection, neutropenia, low B cell number, hypogammaglobulinemia
  • Defects in Intrinsic and Innate Immunity
OMIM
162643
Clinvar variants
Variants in CXCR4
Penetrance
None
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
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 CXCR4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to CXCR4.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to CXCR4.

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 CXCR4 were set to WHIM syndrome, 193670, Myelokathexis, isolated, WHIM syndrome, Warts hypogammaglobulinemia infections and myelokathexis (WHIM), Warts (HPV) infection, neutropenia, low B cell number, hypogammaglobulinemia, Defects in Intrinsic and Innate Immunity

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to CXCR4. 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 CXCR4. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: cxcr4 has been classified as Green List (High Evidence).

20 Apr 2018, Gel status: 4

Set mode of pathogenicity

Louise Daugherty (Genomics England Curator)

Mode of pathogenicity for CXCR4 was changed to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to CXCR4. Panel: Primary immunodeficiency disorders Phenotypes for gene CXCR4 were set to WHIM syndrome, 193670, Myelokathexis, isolated, WHIM syndrome, Warts hypogammaglobulinemia infections and myelokathexis (WHIM)

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene CXCR4 were set to WHIM syndrome, 193670, Myelokathexis, isolated, WHIM syndrome

17 Apr 2018, Gel status: 4

Added New Source, Set mode of inheritance, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to CXCR4. Panel: Primary immunodeficiency disorders Model of inheritance for gene CXCR4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene CXCR4 were set to WHIM syndrome, 193670, Myelokathexis, isolated, WHIM syndrome

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

CXCR4 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Congenital neutropaenia v1.22

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

CXCR4 was created by Louise Daugherty