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Primary immunodeficiency

Gene: MS4A1

Red List (low evidence)

MS4A1 (membrane spanning 4-domains A1)
EnsemblGeneIds (GRCh38): ENSG00000156738
EnsemblGeneIds (GRCh37): ENSG00000156738
OMIM: 112210, Gene2Phenotype
MS4A1 is in 3 panels

3 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

Single patient reported
Created: 29 Jun 2018, 2:46 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Sarah Leigh (Genomics England Curator)

Red List (low evidence)

Associated with phenotype in OMIM and not in Gen2Phen. A single complex variant identified in one case.
Created: 1 May 2018, 1:40 p.m.

Louise Daugherty (Genomics England Curator)

I don't know

Comment on list classification: Changed from Amber to Red based on external clinical expert review and review of the literature. Only a single case has been reported. Gene is pertinent on Victorian Clinical Genetics Services and GRID panel for Immunological disorders. However gene not present on any other PID related panels or within ESID or IUIS classifications. Request evidences / immunological association of this gene from Victorian Clinical Genetics Services and GRID
Created: 4 Jul 2018, 1:23 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): MS4A1 .PanelApp HGNC gene symbol check: MS4A1 . IUIS Disease: CD20 deficiency . IUIS Inheritance: AR .T cells: N/A, .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.
CD20
Created: 27 Jun 2018, 7:31 p.m.
Comment on phenotypes: added in ESID category
Created: 2 May 2018, 10:30 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: CD20, PanelApp HGNC gene symbol check: MS4A1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Predominantly antibody disorders / Hypogammaglobulinemias / Common variable immunodeficiency disorders (CVID)
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: MS4A1, GRID_Gene_Symbol: MS4A1, GRID_Transcript_ENS_Community submitted: ENST00000534668, GRID_Transcript_RefSeq: NM_152866.2, GRID_Transcript_ENS_used_on_Production: ENST00000534668
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • IUIS Classification December 2019
  • Expert Review Red
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Common variable immunodeficiency disorders (CVID)
  • Recurrent infections
  • Immunodeficiency, common variable, 5 613495
  • Predominantly Antibody Deficiencies
OMIM
112210
Clinvar variants
Variants in MS4A1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to MS4A1. Added phenotypes Recurrent infections; Predominantly Antibody Deficiencies for gene: MS4A1 Publications for gene MS4A1 were updated from 20038800; 27250108 to 32048120; 27250108; 20038800; 32086639

12 Jul 2018, Gel status: 1

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.

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ms4a1 has been classified as Red List (Low Evidence).

4 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: ms4a1 has been classified as Red List (Low Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene MS4A1 were set to Immunodeficiency, common variable, 5 613495, Common variable immunodeficiency disorders (CVID), 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 MS4A1. 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 MS4A1. Panel: Primary immunodeficiency disorders

2 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for MS4A1 were set to Immunodeficiency, common variable, 5 613495; Common variable immunodeficiency disorders (CVID)

2 May 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for MS4A1 were set to Immunodeficiency, common variable, 5 613495; Common variable immunodeficiency disorders (CVID)

1 May 2018, Gel status: 2

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

1 May 2018, Gel status: 1

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

1 May 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for MS4A1 were set to 20038800; 27250108

1 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for MS4A1 were set to Immunodeficiency, common variable, 5 613495

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to MS4A1. 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 MS4A1. Panel: Primary immunodeficiency disorders Phenotypes for gene MS4A1 were set to Immunodeficiency, common variable, 5, Common variable immunodeficiency disorders (CVID)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene MS4A1 were set to Immunodeficiency, common variable, 5

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

MS4A1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

MS4A1 was created by Louise Daugherty