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Primary immunodeficiency

Gene: MAGT1

Green List (high evidence)

MAGT1 (magnesium transporter 1)
EnsemblGeneIds (GRCh38): ENSG00000102158
EnsemblGeneIds (GRCh37): ENSG00000102158
OMIM: 300715, Gene2Phenotype
MAGT1 is in 9 panels

7 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, 1:20 p.m. | Last Modified: 14 Oct 2020, 1:20 p.m.
Panel Version: 2.275
The following PubMed IDs were added to entity MAGT1: 21796205;29635109. These publications have been associated with OMIM phenotype MIM#300853, which is listed for this entity, by the immunedysregulation 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

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): MAGT1 .PanelApp HGNC gene symbol check: MAGT1 . IUIS Disease: MAGT1 deficiency (XMEN) . IUIS Inheritance: XL .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: EBV infection, lymphoma, viral infections, respiratory and GI infections. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: Susceptibility to EBV and Lymphoproliferative Conditions
Created: 2 Jul 2018, 10:35 a.m.
Transfer of reviews on publications that were in the publications section. Review made by Ellen McDonagh (Genomics England Curator), 3 Jun 2016. PMID: 21796205 - two young brothers with a 10bp deletion not present in the mother's cDNA or 100 normal individuals, present in the grandmother and great-grandmother of the patients. MAGT1 protein was undetectable in the patient's cells, screening of a third unrelated patient identified a nonsense mutation in exon 3 23846901 27095930 (2 patients with T-B+NK+ combined immunodeficiency) PMID: 25956530 case study of a 17 year old boy with severe autoimmune disorders and Hodgkin lymphoma mimicking autoimmune lymphoproliferative syndrome with a hemizygous c.555dup variant PMID: 25504528 case of a 58-year old Caucasian male and his nephew, identified novel variant c.712C > T, p.R238X (though unclear whether other unaffected family members had this variant) PMID: 25205404 clinical utility gene card describes 7 patients PMID: 24550228 - define XMEN disease, characterised by loss-of-function mutations in MAGT1. PMID: 23871722 association with X-linked intellectual disability is questioned PMID: 21983175 functional study
Created: 18 Apr 2018, 3:45 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: MAGT1, PanelApp HGNC gene symbol check: MAGT1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: MAGT1, GRID_Gene_Symbol: MAGT1, GRID_Transcript_ENS_Community submitted: ENST00000358075, GRID_Transcript_RefSeq: NM_032121.5, GRID_Transcript_ENS_used_on_Production: ENST00000358075
Created: 17 Apr 2018, 12:12 p.m.

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Ellen McDonagh (Genomics England Curator)

Comment on list classification: Added by an expert reviewer, with a second green review. Multiple cases reported for association with XMEN syndrome/disease.
Created: 3 Jun 2016, 2:47 p.m.

William Rae (University Hospital Southampton NHS Foundation Trust)

Green List (high evidence)

Mode of inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females

Phenotypes
Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function

Publications

  • Mg2+ regulates cytotoxic functions of NK and CD8 T cells in chronic EBV infection through NKG2D.Science. 2013 Jul 12
  • 341(6142):186-91

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
  • GOSH PID v.8.0
  • Combined B and T cell defect v1.12
Phenotypes
  • Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia 300853
  • Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function
  • XMEN syndrome
  • Immunodeficiency, X-linked, with magnesium defect
  • Epstein-Barr virus infection and neoplasia (XMEN)
  • Combined immunodeficiency
  • EBV infection, lymphoma, viral infections, respiratory and GI infections
  • Diseases of Immune Dysregulation
OMIM
300715
Clinvar variants
Variants in MAGT1
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: magt1 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 MAGT1. Publications for gene MAGT1 were updated from 21796205; 23846901; 27095930; 25956530; 25504528; 25205404; 24550228; 23871722; 21983175 to 25205404; 27095930; 25956530; 23846901; 21796205; 25504528; 29635109; 23871722; 21983175; 24550228 Rating Changed from Green List (high evidence) to Red List (low evidence)

22 Sep 2020, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: MAGT1 were changed from Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia; Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; XMEN syndrome; Immunodeficiency, X-linked, with magnesium defect; Epstein-Barr virus infection and neoplasia (XMEN); Combined immunodeficiency; EBV infection, lymphoma, viral infections, respiratory and GI infections; Diseases of Immune Dysregulation; Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, 300853 to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia 300853; Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; XMEN syndrome; Immunodeficiency, X-linked, with magnesium defect; Epstein-Barr virus infection and neoplasia (XMEN); Combined immunodeficiency; EBV infection, lymphoma, viral infections, respiratory and GI infections; Diseases of Immune Dysregulation

22 Sep 2020, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: MAGT1 were changed from Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia; Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; XMEN syndrome; Immunodeficiency, X-linked, with magnesium defect; Epstein-Barr virus infection and neoplasia (XMEN); Combined immunodeficiency; EBV infection, lymphoma, viral infections, respiratory and GI infections; Diseases of Immune Dysregulation to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia; Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; XMEN syndrome; Immunodeficiency, X-linked, with magnesium defect; Epstein-Barr virus infection and neoplasia (XMEN); Combined immunodeficiency; EBV infection, lymphoma, viral infections, respiratory and GI infections; Diseases of Immune Dysregulation; Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, 300853

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to MAGT1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to MAGT1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to MAGT1.

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 MAGT1 were set to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function, XMEN syndrome, Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia (XMEN), Combined immunodeficiency, EBV infection, lymphoma, viral infections, respiratory and GI infections, Diseases of Immune Dysregulation

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to MAGT1. 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 MAGT1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 4

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: magt1 has been classified as Green List (High Evidence).

20 Apr 2018, Gel status: 4

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for MAGT1 was changed from Unknown to X-LINKED: hemizygous mutation in males, biallelic mutations in females

20 Apr 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for MAGT1 were set to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia; Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function; XMEN syndrome; Immunodeficiency, X-linked, with magnesium defect; Epstein-Barr virus infection and neoplasia (XMEN); Combined immunodeficiency

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to MAGT1. Panel: Primary immunodeficiency disorders Phenotypes for gene MAGT1 were set to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function, XMEN syndrome, Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia (XMEN), Epstein-Barr virus infection and neoplasia (XMEN), Combined immunodeficiency

17 Apr 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene MAGT1 were set to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function, XMEN syndrome, Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia (XMEN), Epstein-Barr virus infection and neoplasia (XMEN)

17 Apr 2018, Gel status: 4

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

GRID V2.0 was added to MAGT1. Panel: Primary immunodeficiency disorders Phenotypes for gene MAGT1 were set to Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia, Chronic active EBV, lymphoproliferation, combined immunodeficiency, impaired t cell function, XMEN syndrome, Immunodeficiency, X-linked, with magnesium defect, Epstein-Barr virus infection and neoplasia (XMEN)

6 Apr 2018, Gel status: 4

Clear Sources

Louise Daugherty (Genomics England Curator)

MAGT1 Source: GOSH PID 20171169 was removed from gene: MAGT1

6 Apr 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

GOSH PID v.8.0 was added to MAGT1. Panel: Primary immunodeficiency disorders

29 Mar 2018, Gel status: 4

Added New Source, Set mode of inheritance

Louise Daugherty (Genomics England Curator)

GOSH PID 20171169 was added to MAGT1. Panel: Primary immunodeficiency disorders Model of inheritance for gene MAGT1 was set to Unknown

29 Mar 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

MAGT1 was added to Primary immunodeficiency disorders panel. Sources: Expert Review Green, Combined B and T cell defect v1.12

29 Mar 2018, Gel status: 4

Created

Louise Daugherty (Genomics England Curator)

MAGT1 was created by Louise Daugherty