Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: FAT4Comment 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, 12:55 p.m. | Last Modified: 14 Oct 2020, 12:55 p.m.
Panel Version: 2.251
The following PubMed IDs were added to gene FAT4 (OMIM gene MIM#612411): 24056717;22469822;22473091;24913602. 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
agree with green geneCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Hennekam-lymphangiectasia-lymphedema syndrome; Van Maldergem syndrome 2
Publications
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
Comment on list classification: Changed Amber to Green from external review comment and further publications to support gene-disease association.Created: 3 Jul 2018, 12:16 p.m.
Hennekam syndrome is an inherited disorder resulting from malformation of the lymphatic system, which is part of both the circulatory system and immune system.Created: 3 Jul 2018, 12:02 p.m.
Comment on publications: Added publications suggested from external expert review to support upgrading of the gene to GreenCreated: 3 Jul 2018, 11:56 a.m.
Comment on phenotypes: added phenotype form OMIM and MIMidCreated: 3 Jul 2018, 11:56 a.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): FAT4 .PanelApp HGNC gene symbol check: FAT4 . IUIS Disease: Hennekam-lymphangiectasia-lymphedema syndrome due to FAT4 deficiency . IUIS Inheritance: AR .T cells: Normal, .B cells: Low/variable, .IUIS Other affected cells: N/A. IUIS Associated features: Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Other Combined immunodeficiencies with associated or syndromic featuresCreated: 2 Jul 2018, 10:35 a.m.
Comment on list classification: 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 from Victorian Clinical Genetics Services. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1. No disorder or MOI was listed in the submitted list.Created: 26 Jun 2018, 12:46 p.m.
Gene: fat4 has been classified as Green List (High Evidence).
Source Other was added to FAT4. Publications for gene FAT4 were updated from 24913602; 25616299; 29681106 to 29681106; 22473091; 22469822; 25616299; 24056717; 24913602 Rating Changed from Green List (high evidence) to Red List (low evidence)
Source NHS GMS was added to FAT4.
Source North West GLH was added to FAT4.
Source London North GLH was added to FAT4.
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.
Gene: fat4 has been classified as Green List (High Evidence).
Gene: fat4 has been classified as Green List (High Evidence).
Phenotypes for gene: FAT4 were set to Hennekam lymphangiectasia-lymphedema syndrome 2, 616006; Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features; Combined immunodeficiencies with associated or syndromic features
Publications for gene: FAT4 were set to 24913602; 25616299; 29681106
Publications for gene: FAT4 were set to 24913602
Phenotypes for gene: FAT4 were set to Hennekam lymphangiectasia-lymphedema syndrome 2, 616006; Van Maldergem syndrome 2, 615546; Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features; Combined immunodeficiencies with associated or syndromic features
Mode of inheritance for gene: FAT4 was changed from to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene FAT4 were set to Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features, Combined immunodeficiencies with associated or syndromic features
IUIS Classification February 2018 was added to FAT4. Panel: Primary immunodeficiency disorders
Gene: fat4 has been classified as Amber List (Moderate Evidence).
FAT4 was added to Primary immunodeficiency disorders panel. Sources: Victorian Clinical Genetics Services
FAT4 was created by Louise Daugherty