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Primary immunodeficiency

Gene: TNFSF12

Red List (low evidence)

TNFSF12 (TNF superfamily member 12)
EnsemblGeneIds (GRCh38): ENSG00000239697
EnsemblGeneIds (GRCh37): ENSG00000239697
OMIM: 602695, Gene2Phenotype
TNFSF12 is in 3 panels

2 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

one kindred only
Created: 29 Jun 2018, 3:45 p.m.

Louise Daugherty (Genomics England Curator)

I don't know

Comment on list classification: Changed from Amber to Red until more info to support gene-disease association. Currently only one case reported in literature, the variant being VUS. Request evidences / immunological association of this gene from Victorian Clinical Genetics Services and GRID
Created: 5 Jul 2018, 2:20 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): TNFSF12 .PanelApp HGNC gene symbol check: TNFSF12 . IUIS Disease: TWEAK deficiency . IUIS Inheritance: AD .T cells: N/A, .B cells: N/A, .IUIS Other affected cells: N/A. IUIS Associated features: Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia. 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.
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: 19 Apr 2018, 11:50 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: TWEAK, PanelApp HGNC gene symbol check: TNFSF12, 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: TNFSF12, GRID_Gene_Symbol: TNFSF12, GRID_Transcript_ENS_Community submitted: ENST00000293825, GRID_Transcript_RefSeq: NM_003809.2, GRID_Transcript_ENS_used_on_Production: ENST00000293825
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
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)
  • Immunodeficiency, common variable with lack of anti-pneumococcal antibody
  • Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia
  • Predominantly Antibody Deficiencies
  • Pneumonia, bacterial infections, warts, thrombocytopenia
OMIM
602695
Clinvar variants
Variants in TNFSF12
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 TNFSF12. Added phenotypes Predominantly Antibody Deficiencies; Pneumonia, bacterial infections, warts, thrombocytopenia for gene: TNFSF12 Publications for gene TNFSF12 were updated from 23493554 to 32048120; 23493554; 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.

5 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: tnfsf12 has been classified as Red List (Low Evidence).

5 Jul 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: TNFSF12 were set to 23493554

5 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: tnfsf12 has been classified as Red List (Low Evidence).

5 Jul 2018, Gel status: 2

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: TNFSF12 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TNFSF12 were set to Immunodeficiency, common variable with lack of anti-pneumococcal antibody, Common variable immunodeficiency disorders (CVID), Pneumonia, bacterial infections, warts, thrombocytopenia. neutropenia, Predominantly Antibody Deficiencies

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to TNFSF12. 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 TNFSF12. Panel: Primary immunodeficiency disorders

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to TNFSF12. Panel: Primary immunodeficiency disorders Phenotypes for gene TNFSF12 were set to Immunodeficiency, common variable with lack of anti-pneumococcal antibody, Common variable immunodeficiency disorders (CVID)

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TNFSF12 were set to Immunodeficiency, common variable with lack of anti-pneumococcal antibody

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

TNFSF12 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

TNFSF12 was created by Louise Daugherty