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Primary immunodeficiency

Gene: JAGN1

Green List (high evidence)

JAGN1 (jagunal homolog 1)
EnsemblGeneIds (GRCh38): ENSG00000171135
EnsemblGeneIds (GRCh37): ENSG00000171135
OMIM: 616012, Gene2Phenotype
JAGN1 is in 7 panels

4 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

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
severe congenital neutropenia

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): JAGN1 .PanelApp HGNC gene symbol check: JAGN1 . IUIS Disease: JAGN1 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N. IUIS Associated features: Myeloid maturation arrest, osteopenia. 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 Amber to Green from external review comment and further publications to support gene-disease association
Created: 27 Jun 2018, 10:08 a.m.
Comment on publications: Added publication to support gene-disease association from expert review. More than three pathogenic variants found more than three unrelated cases
Created: 27 Jun 2018, 10:07 a.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 downloaded from ESID Registry. ESID_Gene_original: JAGN1, PanelApp HGNC gene symbol check: JAGN1, 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: JAGN1, GRID_Gene_Symbol: JAGN1, GRID_Transcript_ENS_Community submitted: ENST00000307768, GRID_Transcript_RefSeq: NM_032492.3, GRID_Transcript_ENS_used_on_Production: ENST00000307768
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • North West GLH
  • London North GLH
  • Expert Review Green
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Neutropenia, severe congenital
  • Congenital neutropenia
  • Neutropenia, severe congenital, 6, autosomal recessive,616022
  • severe congenital neutropenia
  • Myeloid maturation arrest, osteopenia
  • Congenital defects of phagocyte number or function
OMIM
616012
Clinvar variants
Variants in JAGN1
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 JAGN1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to JAGN1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to JAGN1.

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 JAGN1 were set to Neutropenia, severe congenital, Congenital neutropenia, Neutropenia, severe congenital, 6, autosomal recessive,616022, severe congenital neutropenia, Myeloid maturation arrest, osteopenia, Congenital defects of phagocyte number or function

27 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: jagn1 has been classified as Green List (High Evidence).

27 Jun 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: JAGN1 were set to Neutropenia, severe congenital; Congenital neutropenia; Neutropenia, severe congenital, 6, autosomal recessive,616022; severe congenital neutropenia

27 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: jagn1 has been classified as Green List (High Evidence).

27 Jun 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: JAGN1 were set to 25129144

27 Jun 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: JAGN1 were set to Neutropenia, severe congenital; Congenital neutropenia; Neutropenia, severe congenital, 6, autosomal recessive,616022

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to JAGN1. 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 JAGN1. Panel: Primary immunodeficiency disorders

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to JAGN1. 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 JAGN1. Panel: Primary immunodeficiency disorders Phenotypes for gene JAGN1 were set to Neutropenia, severe congenital, Congenital neutropenia

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene JAGN1 were set to Neutropenia, severe congenital

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

JAGN1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

JAGN1 was created by Louise Daugherty