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Primary immunodeficiency

Gene: TNFRSF4

Red List (low evidence)

TNFRSF4 (TNF receptor superfamily member 4)
EnsemblGeneIds (GRCh38): ENSG00000186827
EnsemblGeneIds (GRCh37): ENSG00000186827
OMIM: 600315, Gene2Phenotype
TNFRSF4 is in 3 panels

3 reviews

Eleanor Williams (Genomics England Curator)

The following PubMed IDs were added to gene TNFRSF4 (OMIM gene MIM#600315): 23897980. These publications have been associated with the gene by the immunodeficiencies 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

Sophie Hambleton (Newcastle University)

Red List (low evidence)

single patient described
Created: 29 Jun 2018, 3:43 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. Request evidences / immunological association of this gene from Victorian Clinical Genetics Services and GRID
Created: 5 Jul 2018, 2:08 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): TNFRSF4 .PanelApp HGNC gene symbol check: TNFRSF4 . IUIS Disease: OX40 deficiency . IUIS Inheritance: AR .T cells: N/A, .B cells: Nl numbers, low memory B cells, .IUIS Other affected cells: N/A. IUIS Associated features: Impaired immunity to HHV8, Kaposis sarcoma. IUIS Major category: Immunodeficiencies affecting cellular and humoral immunity. IUIS Subcategory: Combined Immunodeficiencies Generally Less Profound than Severe Combined Immunodeficiency
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, 11:51 a.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: OX40, PanelApp HGNC gene symbol check: TNFRSF4, 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: TNFRSF4, GRID_Gene_Symbol: TNFRSF4, GRID_Transcript_ENS_Community submitted: ENST00000379236, GRID_Transcript_RefSeq: NM_003327.3, GRID_Transcript_ENS_used_on_Production: ENST00000379236
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Other
  • IUIS Classification December 2019
  • Expert Review Red
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency
  • Immunodeficiencies affecting cellular and humoral immunity
  • Impaired immunity to HHV8, Kaposis sarcoma
  • Combined immunodeficiency
OMIM
600315
Clinvar variants
Variants in TNFRSF4
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Oct 2020, Gel status: 1

Added New Source, Set publications

Eleanor Williams (Genomics England Curator)

Source Other was added to TNFRSF4. Publications for gene TNFRSF4 were updated from 32048120; 32086639 to 32086639; 23897980; 32048120

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 TNFRSF4. Added phenotypes Impaired immunity to HHV8, Kaposis sarcoma; Immunodeficiencies affecting cellular and humoral immunity for gene: TNFRSF4 Publications for gene TNFRSF4 were updated from to 32048120; 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: tnfrsf4 has been classified as Red List (Low Evidence).

5 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: tnfrsf4 has been classified as Red List (Low Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TNFRSF4 were set to Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency, Combined immunodeficiency, Impaired immunity to HHV8, Kaposis sarcoma, Immunodeficiencies affecting cellular and humoral immunity

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to TNFRSF4. 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 TNFRSF4. 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 TNFRSF4. Panel: Primary immunodeficiency disorders Phenotypes for gene TNFRSF4 were set to Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency, Combined immunodeficiency

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene TNFRSF4 were set to Kaposi's Sarcoma, impaired immunity to HHV8, OX40 deficiency

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

TNFRSF4 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

TNFRSF4 was created by Louise Daugherty